RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-06 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_141 python-lpbuildd_141 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.6. Syncing the system clock with the buildd NTP service... 27 Jan 09:40:08 ntpdate[1911]: adjust time server 10.211.37.1 offset 0.030796 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11930830', '/home/buildd/filecache-default/94f0b0f826e99ad354ce9a7a99ba3c310ddcc327'] Unpacking chroot for build PACKAGEBUILD-11930830 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11930830'] Mounting chroot for build PACKAGEBUILD-11930830 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11930830', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11930830 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11930830', 'amd64'] Updating debian chroot for build PACKAGEBUILD-11930830 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [253 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [102 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [102 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 Packages [1227 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [589 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe amd64 Packages [8089 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4685 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 Packages [135 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [71.8 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 Packages [703 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [316 kB] Fetched 16.4 MB in 4s (3616 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.24 perl-modules-5.24 The following packages will be upgraded: adduser advancecomp apt apt-transport-https base-files base-passwd bash binutils bsdutils ca-certificates cpp cpp-6 debianutils diffutils dmsetup findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libdevmapper1.02.1 libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libisl15 libitm1 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblsan0 liblzma5 libmount1 libmpx2 libnettle6 libnpth0 libp11-kit0 libpng16-16 libquadmath0 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libustr-1.0-1 libuuid1 libwind0-heimdal linux-libc-dev mount multiarch-support openssl perl perl-base pinentry-curses pkg-create-dbgsym sed systemd systemd-sysv tar tzdata ubuntu-keyring util-linux xz-utils zlib1g 110 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 MB of archives. After this operation, 41.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main amd64 base-files amd64 9.6ubuntu9 [57.0 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main amd64 debianutils amd64 4.8.1 [85.7 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main amd64 bash amd64 4.4-2ubuntu1 [624 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main amd64 bsdutils amd64 1:2.29-1ubuntu2 [55.3 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 diffutils amd64 1:3.5-3 [166 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main amd64 findutils amd64 4.6.0+git+20161106-1 [282 kB] Get:7 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 grep amd64 2.27-2 [154 kB] Get:8 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libc6-dev amd64 2.24-7ubuntu2 [2274 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libc-dev-bin amd64 2.24-7ubuntu2 [68.5 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 linux-libc-dev amd64 4.9.0-15.16 [881 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libitm1 amd64 6.3.0-5ubuntu1 [27.9 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc-6-base amd64 6.3.0-5ubuntu1 [17.5 kB] Get:13 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgcc1 amd64 1:6.3.0-5ubuntu1 [38.1 kB] Get:14 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libcc1-0 amd64 6.3.0-5ubuntu1 [31.1 kB] Get:15 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 binutils amd64 2.27.90.20170118-1ubuntu1 [2432 kB] Get:16 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgomp1 amd64 6.3.0-5ubuntu1 [74.0 kB] Get:17 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libatomic1 amd64 6.3.0-5ubuntu1 [9178 B] Get:18 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libasan3 amd64 6.3.0-5ubuntu1 [316 kB] Get:19 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 liblsan0 amd64 6.3.0-5ubuntu1 [117 kB] Get:20 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libtsan0 amd64 6.3.0-5ubuntu1 [261 kB] Get:21 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libubsan0 amd64 6.3.0-5ubuntu1 [108 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libcilkrts5 amd64 6.3.0-5ubuntu1 [40.8 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libmpx2 amd64 6.3.0-5ubuntu1 [11.5 kB] Get:24 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libquadmath0 amd64 6.3.0-5ubuntu1 [132 kB] Get:25 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 g++-6 amd64 6.3.0-5ubuntu1 [7391 kB] Get:26 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libstdc++-6-dev amd64 6.3.0-5ubuntu1 [1423 kB] Get:27 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgcc-6-dev amd64 6.3.0-5ubuntu1 [2309 kB] Get:28 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc-6 amd64 6.3.0-5ubuntu1 [7170 kB] Get:29 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 cpp-6 amd64 6.3.0-5ubuntu1 [6607 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libstdc++6 amd64 6.3.0-5ubuntu1 [402 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main amd64 zlib1g amd64 1:1.2.8.dfsg-4ubuntu1 [50.9 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [240 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main amd64 libisl15 amd64 0.18-1 [545 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libc6 amd64 2.24-7ubuntu2 [2587 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main amd64 libuuid1 amd64 2.29-1ubuntu2 [14.7 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main amd64 libblkid1 amd64 2.29-1ubuntu2 [110 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main amd64 libfdisk1 amd64 2.29-1ubuntu2 [144 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main amd64 libselinux1 amd64 2.6-3 [67.8 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main amd64 util-linux amd64 2.29-1ubuntu2 [911 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main amd64 mount amd64 2.29-1ubuntu2 [129 kB] Get:41 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 perl-modules-5.24 all 5.24.1-1 [2662 kB] Get:42 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libperl5.24 amd64 5.24.1-1 [3473 kB] Get:43 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 perl amd64 5.24.1-1 [219 kB] Get:44 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 perl-base amd64 5.24.1-1 [1341 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/main amd64 sed amd64 4.3-3 [178 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/main amd64 tar amd64 1.29b-1.1 [232 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main amd64 base-passwd amd64 3.5.43 [48.4 kB] Get:48 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 init-system-helpers all 1.47 [37.8 kB] Get:49 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libc-bin amd64 2.24-7ubuntu2 [635 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main amd64 liblzma5 amd64 5.2.2-1.2 [91.0 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main amd64 libapt-pkg5.0 amd64 1.4~beta4ubuntu1 [785 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main amd64 adduser all 3.113+nmu3ubuntu5 [161 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/main amd64 ubuntu-keyring all 2016.10.27 [16.6 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main amd64 apt amd64 1.4~beta4ubuntu1 [1073 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main amd64 libapparmor1 amd64 2.10.95-4ubuntu5.2 [30.2 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/main amd64 libgpg-error0 amd64 1.26-2 [34.6 kB] Get:57 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgcrypt20 amd64 1.7.6-1 [399 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main amd64 libmount1 amd64 2.29-1ubuntu2 [119 kB] Get:59 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu1 [37.5 kB] Get:60 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 systemd amd64 232-10ubuntu1 [2358 kB] Get:61 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libsystemd0 amd64 232-10ubuntu1 [211 kB] Get:62 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 init amd64 1.47 [5832 B] Get:63 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 systemd-sysv amd64 232-10ubuntu1 [13.9 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/main amd64 libsepol1 amd64 2.6-2 [220 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main amd64 libustr-1.0-1 amd64 1.0.4-6 [66.1 kB] Get:66 http://ftpmaster.internal/ubuntu zesty/main amd64 libsemanage-common all 2.6-2 [6794 B] Get:67 http://ftpmaster.internal/ubuntu zesty/main amd64 libsemanage1 amd64 2.6-2 [82.6 kB] Get:68 http://ftpmaster.internal/ubuntu zesty/main amd64 libsmartcols1 amd64 2.29-1ubuntu2 [69.4 kB] Get:69 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libudev1 amd64 232-10ubuntu1 [57.3 kB] Get:70 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[107 kB] Get:80 http://ftpmaster.internal/ubuntu zesty/main amd64 libtasn1-6 amd64 4.10-1 [35.4 kB] Get:81 http://ftpmaster.internal/ubuntu zesty/main amd64 libgnutls30 amd64 3.5.6-4ubuntu2 [626 kB] Get:82 http://ftpmaster.internal/ubuntu zesty/main amd64 libheimbase1-heimdal amd64 1.7~git20160703+dfsg-1ubuntu1 [29.2 kB] Get:83 http://ftpmaster.internal/ubuntu zesty/main amd64 libhcrypto4-heimdal amd64 1.7~git20160703+dfsg-1ubuntu1 [87.2 kB] Get:84 http://ftpmaster.internal/ubuntu zesty/main amd64 libwind0-heimdal amd64 1.7~git20160703+dfsg-1ubuntu1 [48.0 kB] Get:85 http://ftpmaster.internal/ubuntu zesty/main amd64 libhx509-5-heimdal amd64 1.7~git20160703+dfsg-1ubuntu1 [107 kB] Get:86 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libsqlite3-0 amd64 3.16.2-2 [486 kB] Get:87 http://ftpmaster.internal/ubuntu zesty/main amd64 libkrb5-26-heimdal amd64 1.7~git20160703+dfsg-1ubuntu1 [202 kB] Get:88 http://ftpmaster.internal/ubuntu zesty/main amd64 libheimntlm0-heimdal amd64 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http://ftpmaster.internal/ubuntu zesty/main amd64 xz-utils amd64 5.2.2-1.2 [83.2 kB] Get:99 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgssapi-krb5-2 amd64 1.15-1 [120 kB] Get:100 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libkrb5-3 amd64 1.15-1 [275 kB] Get:101 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libkrb5support0 amd64 1.15-1 [31.9 kB] Get:102 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libk5crypto3 amd64 1.15-1 [84.8 kB] Get:103 http://ftpmaster.internal/ubuntu zesty/main amd64 libcurl3-gnutls amd64 7.51.0-1ubuntu1 [188 kB] Get:104 http://ftpmaster.internal/ubuntu zesty/main amd64 apt-transport-https amd64 1.4~beta4ubuntu1 [34.5 kB] Get:105 http://ftpmaster.internal/ubuntu zesty/main amd64 openssl amd64 1.0.2g-1ubuntu10 [491 kB] Get:106 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 ca-certificates all 20161130 [193 kB] Get:107 http://ftpmaster.internal/ubuntu zesty/main amd64 libpng16-16 amd64 1.6.28-1 [172 kB] Get:108 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 advancecomp amd64 1.23-1 [197 kB] Get:109 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 cpp amd64 4:6.3.0-1ubuntu3 [27.5 kB] Get:110 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc amd64 4:6.3.0-1ubuntu3 [5172 B] Get:111 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 g++ amd64 4:6.3.0-1ubuntu3 [1472 B] Get:112 http://ftpmaster.internal/ubuntu zesty/main amd64 pkg-create-dbgsym all 0.73 [8952 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 MB in 7s (7964 kB/s) (Reading database ... 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Setting up binutils (2.27.90.20170118-1ubuntu1) ... Setting up libc-dev-bin (2.24-7ubuntu2) ... Setting up ca-certificates (20161130) ... Updating certificates in /etc/ssl/certs... 10 added, 10 removed; done. Setting up libc6-dev:amd64 (2.24-7ubuntu2) ... Setting up libslang2:amd64 (2.3.1-5ubuntu1) ... Setting up libassuan0:amd64 (2.4.3-2) ... Setting up libitm1:amd64 (6.3.0-5ubuntu1) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up libgcc-6-dev:amd64 (6.3.0-5ubuntu1) ... Setting up libstdc++-6-dev:amd64 (6.3.0-5ubuntu1) ... Setting up libwind0-heimdal:amd64 (1.7~git20160703+dfsg-1ubuntu1) ... Setting up init (1.47) ... Setting up libasn1-8-heimdal:amd64 (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libhcrypto4-heimdal:amd64 (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libhx509-5-heimdal:amd64 (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libhogweed4:amd64 (3.3-1) ... Setting up libisl15:amd64 (0.18-1) ... Setting up pinentry-curses (1.0.0-1) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11930830', 'amd64', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=zesty-proposed', '--purge=never', '--nolog', '-A', 'python-pysam_0.10.0+ds-1ubuntu1.dsc'] Initiating build PACKAGEBUILD-11930830 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-06.buildd +==============================================================================+ | python-pysam 0.10.0+ds-1ubuntu1 (amd64) 27 Jan 2017 09:41 | +==============================================================================+ Package: python-pysam Version: 0.10.0+ds-1ubuntu1 Source Version: 0.10.0+ds-1ubuntu1 Distribution: zesty-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-pysam-NQz0GF/python-pysam-0.10.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-NQz0GF' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11930830/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.10.0+ds-1ubuntu1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-5FdFud/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-5FdFud/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5FdFud/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-5FdFud/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5FdFud/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-5FdFud/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (230 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5FdFud/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-WObSP8/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-WObSP8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-WObSP8/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-WObSP8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-WObSP8/apt_archive ./ Sources [299 B] Get:5 copy:/<>/resolver-WObSP8/apt_archive ./ Packages [620 B] Fetched 3038 B in 0s (240 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts1 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts1 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 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Unpacking sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... Setting up libhts1:amd64 (1.3.2-2ubuntu1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up libhts-dev:amd64 (1.3.2-2ubuntu1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.51.0-2) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-1ubuntu2) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up libgsl2:amd64 (2.3+dfsg-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-5) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ... Setting up libmagic-mgc (1:5.29-3) ... Setting up libmagic1:amd64 (1:5.29-3) ... Setting up libcroco3:amd64 (0.6.11-2) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Setting up libexpat1-dev:amd64 (2.2.0-2) ... Setting up tabix (1.3.2-2ubuntu1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up samtools (1.3.1-3) ... Setting up bcftools (1.3.1-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-4ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.029-2) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libpython3.5-stdlib:amd64 (3.5.3-1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.29-3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:amd64 (2.7.13-2) ... Setting up automake (1:1.15-5ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:amd64 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1) ... Setting up libpython-dev:amd64 (2.7.13-2) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:amd64 (3.5.3-1) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:amd64 (2.7.13-2) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up libpython3.5-dev:amd64 (3.5.3-1) ... Setting up cython (0.25.2-1) ... Setting up python3.5-dev (3.5.3-1) ... Setting up python-nose (1.3.7-2) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:amd64 (3.5.3-1) ... Setting up python-setuptools (33.1.1-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:amd64 (3.5.3-1) ... Setting up dh-autoreconf (13) ... Setting up python3 (3.5.3-1) ... Setting up python3-dev (3.5.3-1) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up dh-strip-nondeterminism (0.029-2) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-all (3.5.3-1) ... Setting up cython3 (0.25.2-1) ... Setting up python3-setuptools (33.1.1-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up python3-all-dev (3.5.3-1) ... Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-59-generic amd64 (x86_64) Toolchain package versions: binutils_2.27.90.20170118-1ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.3.0-5ubuntu1 gcc-6_6.3.0-5ubuntu1 libc6-dev_2.24-7ubuntu2 libstdc++-6-dev_6.3.0-5ubuntu1 libstdc++6_6.3.0-5ubuntu1 linux-libc-dev_4.9.0-15.16 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4~beta4ubuntu1 apt-transport-https_1.4~beta4ubuntu1 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20161112.1 base-files_9.6ubuntu9 base-passwd_3.5.43 bash_4.4-2ubuntu1 bcftools_1.3.1-1 binutils_2.27.90.20170118-1ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20161130 coreutils_8.25-2ubuntu2 cpp_4:6.3.0-1ubuntu3 cpp-6_6.3.0-5ubuntu1 cython_0.25.2-1 cython3_0.25.2-1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8.1 dh-autoreconf_13 dh-python_2.20170125 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-3 dmsetup_2:1.02.136-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.29-3 findutils_4.6.0+git+20161106-1 g++_4:6.3.0-1ubuntu3 g++-6_6.3.0-5ubuntu1 gcc_4:6.3.0-1ubuntu3 gcc-6_6.3.0-5ubuntu1 gcc-6-base_6.3.0-5ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-4ubuntu1 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.2 libapt-pkg5.0_1.4~beta4ubuntu1 libarchive-zip-perl_1.59-1 libasan3_6.3.0-5ubuntu1 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libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.16.2-2 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu10 libstdc++-6-dev_6.3.0-5ubuntu1 libstdc++6_6.3.0-5ubuntu1 libsystemd0_232-10ubuntu1 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_6.3.0-5ubuntu1 libubsan0_6.3.0-5ubuntu1 libudev1_232-10ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_1.7~git20160703+dfsg-1ubuntu1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_4.9.0-15.16 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-7ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu10 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1-1 perl-base_5.24.1-1 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1-1 pinentry-curses_1.0.0-1 pkg-create-dbgsym_0.73 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_33.1.1-1 python-setuptools_33.1.1-1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1 python3-all_3.5.3-1 python3-all-dev_3.5.3-1 python3-dev_3.5.3-1 python3-minimal_3.5.3-1 python3-nose_1.3.7-2 python3-pkg-resources_33.1.1-1 python3-setuptools_33.1.1-1 python3.5_3.5.3-1 python3.5-dev_3.5.3-1 python3.5-minimal_3.5.3-1 readline-common_7.0-0ubuntu2 samtools_1.3.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.3-3 sensible-utils_0.0.9 systemd_232-10ubuntu1 systemd-sysv_232-10ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.3.2-2ubuntu1 tar_1.29b-1.1 tzdata_2016j-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-4ubuntu1 zlib1g-dev_1:1.2.8.dfsg-4ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Jan 27 09:37:09 2017 UTC gpgv: using RSA key gpgv: issuer "ginggs@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.10.0+ds-1ubuntu1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.10.0+ds dpkg-source: info: unpacking python-pysam_0.10.0+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.10.0+ds-1ubuntu1.debian.tar.xz dpkg-source: info: applying rpath.patch dpkg-source: info: applying htslib-external-config.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/python-pysam-0.10.0+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/python-pysam-0.10.0+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.10.0+ds-1ubuntu1 dpkg-buildpackage: info: source distribution zesty dpkg-source --before-build python-pysam-0.10.0+ds dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c dh clean --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' dh_auto_clean I: pybuild base:184: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.5 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ samtools/config.h make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.5 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-amd64-2.7 creating build/temp.linux-amd64-2.7/pysam x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-amd64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libchtslib.o build/temp.linux-amd64-2.7/pysam/htslib_util.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension creating build/temp.linux-amd64-2.7/samtools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-amd64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcsamfile.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-amd64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcalignmentfile.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-amd64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcalignedsegment.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-amd64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-amd64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libctabix.o build/temp.linux-amd64-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-amd64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libctabixproxies.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-amd64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.66’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcvcf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-amd64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcbcf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-amd64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcbgzf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-amd64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension creating build/temp.linux-amd64-2.7/bcftools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-amd64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:10530:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-amd64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] #warning "No curses library is available; tview with curses is disabled." ^~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘info_rules_init’: bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’: bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~ bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-amd64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcutils.o build/temp.linux-amd64-2.7/pysam/pysam_util.o build/temp.linux-amd64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-amd64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-amd64-2.7/samtools/sample.c.pysam.o build/temp.linux-amd64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-amd64-2.7/samtools/padding.c.pysam.o build/temp.linux-amd64-2.7/samtools/phase.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-amd64-2.7/samtools/errmod.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-amd64-2.7/samtools/faidx.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-amd64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-amd64-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam.c.pysam.o build/temp.linux-amd64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-amd64-2.7/samtools/dict.c.pysam.o build/temp.linux-amd64-2.7/samtools/stats.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-amd64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-amd64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-amd64-2.7/bcftools/main.c.pysam.o build/temp.linux-amd64-2.7/bcftools/em.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-amd64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-amd64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-amd64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-amd64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-amd64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-amd64-2.7/bcftools/filter.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-amd64-2.7/bcftools/version.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-amd64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-amd64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-amd64-2.7/bcftools/convert.c.pysam.o -Lpysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so I: pybuild base:184: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-amd64-3.5 creating build/temp.linux-amd64-3.5/pysam x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libchtslib.c -o build/temp.linux-amd64-3.5/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-amd64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libchtslib.o build/temp.linux-amd64-3.5/pysam/htslib_util.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension creating build/temp.linux-amd64-3.5/samtools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcsamfile.c -o build/temp.linux-amd64-3.5/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-amd64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-amd64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-amd64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcsamfile.o build/temp.linux-amd64-3.5/pysam/htslib_util.o build/temp.linux-amd64-3.5/pysam/samfile_util.o build/temp.linux-amd64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignmentfile.c -o build/temp.linux-amd64-3.5/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-amd64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-amd64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-amd64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcalignmentfile.o build/temp.linux-amd64-3.5/pysam/htslib_util.o build/temp.linux-amd64-3.5/pysam/samfile_util.o build/temp.linux-amd64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignedsegment.c -o build/temp.linux-amd64-3.5/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-amd64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-amd64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-amd64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcalignedsegment.o build/temp.linux-amd64-3.5/pysam/htslib_util.o build/temp.linux-amd64-3.5/pysam/samfile_util.o build/temp.linux-amd64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libctabix.c -o build/temp.linux-amd64-3.5/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-amd64-3.5/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libctabix.o build/temp.linux-amd64-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/libctabixproxies.c -o build/temp.linux-amd64-3.5/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libctabixproxies.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcvcf.c -o build/temp.linux-amd64-3.5/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.67’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcvcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbcf.c -o build/temp.linux-amd64-3.5/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcbcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbgzf.c -o build/temp.linux-amd64-3.5/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcbgzf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcfaidx.c -o build/temp.linux-amd64-3.5/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcfaidx.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-x86_64-linux-gnu.so skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension creating build/temp.linux-amd64-3.5/bcftools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcutils.c -o build/temp.linux-amd64-3.5/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-amd64-3.5/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] #warning "No curses library is available; tview with curses is disabled." ^~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-amd64-3.5/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘info_rules_init’: bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’: bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~ bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-amd64-3.5/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/pysam/libcutils.o build/temp.linux-amd64-3.5/pysam/pysam_util.o build/temp.linux-amd64-3.5/samtools/bamtk.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_color.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-amd64-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-amd64-3.5/samtools/sample.c.pysam.o build/temp.linux-amd64-3.5/samtools/cut_target.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-amd64-3.5/samtools/padding.c.pysam.o build/temp.linux-amd64-3.5/samtools/phase.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-amd64-3.5/samtools/errmod.c.pysam.o build/temp.linux-amd64-3.5/samtools/sam_view.c.pysam.o build/temp.linux-amd64-3.5/samtools/faidx.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-amd64-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_import.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_md.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_index.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-amd64-3.5/samtools/bedcov.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-3.5/samtools/bedidx.c.pysam.o build/temp.linux-amd64-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-amd64-3.5/samtools/sam.c.pysam.o build/temp.linux-amd64-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-amd64-3.5/samtools/dict.c.pysam.o build/temp.linux-amd64-3.5/samtools/stats.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-amd64-3.5/samtools/sam_header.c.pysam.o build/temp.linux-amd64-3.5/samtools/bam_split.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-amd64-3.5/bcftools/ccall.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-amd64-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-amd64-3.5/bcftools/HMM.c.pysam.o build/temp.linux-amd64-3.5/bcftools/main.c.pysam.o build/temp.linux-amd64-3.5/bcftools/em.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-amd64-3.5/bcftools/consensus.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-amd64-3.5/bcftools/mcall.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-amd64-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-amd64-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-amd64-3.5/bcftools/prob1.c.pysam.o build/temp.linux-amd64-3.5/bcftools/filter.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-amd64-3.5/bcftools/version.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-amd64-3.5/bcftools/tabix.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-amd64-3.5/bcftools/kmin.c.pysam.o build/temp.linux-amd64-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-amd64-3.5/bcftools/convert.c.pysam.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-x86_64-linux-gnu.so debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS rg_with_tab.sam > rg_with_tab.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.bam samtools index tag_bug.bam samtools index ex9_fail.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index test_unaligned.bam samtools index ex6.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index ex5.bam samtools index rg_with_tab.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index example_user_header.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' dh_auto_test I: pybuild base:184: cd /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose reference bases should always be the same nucleotide ... ok testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok check comparison functions. ... ok testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok see issue 26 ... ok testHashing (AlignedSegment_test.TestAlignedSegment) ... ok build an example read. ... ok issue 176: retrieving length without query sequence ... ok testPositions (AlignedSegment_test.TestAlignedSegment) ... ok see issue 62 ... ok testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok testAsString (AlignedSegment_test.TestAsString) ... ok testStats (AlignedSegment_test.TestCigarStats) ... ok testCopy (AlignedSegment_test.TestCopy) ... ok testDeepCopy (AlignedSegment_test.TestCopy) ... ok testAddTags (AlignedSegment_test.TestTags) ... ok testAddTagsType (AlignedSegment_test.TestTags) ... ok testArrayTags (AlignedSegment_test.TestTags) ... ok testEmptyTag (AlignedSegment_test.TestTags) ... ok testMDTagComplex (AlignedSegment_test.TestTags) ... ok testMDTagDeletions (AlignedSegment_test.TestTags) ... ok testMDTagInsertions (AlignedSegment_test.TestTags) ... ok testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok testMissingTag (AlignedSegment_test.TestTags) ... ok testSetTag (AlignedSegment_test.TestTags) ... ok test for tag parsing ... ok testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok test BAM autodetection. ... ok test CRAM autodetection. ... ok test SAM autodetection. ... ok testReadTags (AlignmentFile_test.TestBTagBam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok testReadTags (AlignmentFile_test.TestBTagSam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok testClipping (AlignmentFile_test.TestClipping) ... ok testManager (AlignmentFile_test.TestContextManager) ... ok test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok testBadContig (AlignmentFile_test.TestExceptions) ... ok testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok testMissingFile (AlignmentFile_test.TestExceptions) ... ok testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok see issue 44 ... ok testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<>/python-pysam-0.10.0+ds/tests/pysam_data/ex1.bam.bai ok testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok test_all (AlignmentFile_test.TestFindIntrons) ... ok test_first (AlignmentFile_test.TestFindIntrons) ... ok test_total (AlignmentFile_test.TestFindIntrons) ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok testBAM2BAM (AlignmentFile_test.TestIO) ... ok testBAM2CRAM (AlignmentFile_test.TestIO) ... ok testBAM2SAM (AlignmentFile_test.TestIO) ... ok see issue 116 ... ok see issue 116 ... ok see issue 117 ... ok testCRAM2BAM (AlignmentFile_test.TestIO) ... ok testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok testCRAM2SAM (AlignmentFile_test.TestIO) ... ok test that access to a closed samfile raises ValueError. ... ok testEmptyBAM (AlignmentFile_test.TestIO) ... ok testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok test IteratorRowHead ... ok testOpenFromFilename (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok testReadSamWithoutHeader (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok read from bam file without index. ... ok testSAM2BAM (AlignmentFile_test.TestIO) ... ok testSAM2CRAM (AlignmentFile_test.TestIO) ... ok testSAM2SAM (AlignmentFile_test.TestIO) ... ok testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok read from uncompressed BAM file, see issue #43 ... ok see issue 131 ... ok testStart (AlignmentFile_test.TestIteratorColumn2) ... ok test if PileupRead can be printed. ... ok see issue 107. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok when creating a read with a large entry in the tag field ... ok testBAM (AlignmentFile_test.TestLargeOptValues) ... ok testSAM (AlignmentFile_test.TestLargeOptValues) ... ok testFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail2 (AlignmentFile_test.TestLogging) ... ok testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok testAllStepper (AlignmentFile_test.TestPileup) ... ok testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok testArrayTags (AlignmentFile_test.TestTagParsing) ... ok testCigar (AlignmentFile_test.TestTagParsing) ... ok testCigarString (AlignmentFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok testTruncatedBam (AlignmentFile_test.TestTruncatedBAM) ... [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes ok See comments for pull request at ... ok testBAM (AlignmentFile_test.TestUnmappedReads) ... ok testVerbosity (AlignmentFile_test.TestVerbosity) ... ok testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok testARcigar (SamFile_test.BasicTestBAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestBAMFetch) ... ok testARflag (SamFile_test.BasicTestBAMFetch) ... ok testARisize (SamFile_test.BasicTestBAMFetch) ... ok testARmapq (SamFile_test.BasicTestBAMFetch) ... ok testARmpos (SamFile_test.BasicTestBAMFetch) ... ok testARmrnm (SamFile_test.BasicTestBAMFetch) ... ok testARpos (SamFile_test.BasicTestBAMFetch) ... ok testARqname (SamFile_test.BasicTestBAMFetch) ... ok testARqqual (SamFile_test.BasicTestBAMFetch) ... ok testARqual (SamFile_test.BasicTestBAMFetch) ... ok testARquery (SamFile_test.BasicTestBAMFetch) ... ok testARrname (SamFile_test.BasicTestBAMFetch) ... ok testARseq (SamFile_test.BasicTestBAMFetch) ... ok testAddTags (SamFile_test.BasicTestBAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestBAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestBAMFetch) ... ok testOpt (SamFile_test.BasicTestBAMFetch) ... ok testPairedBools (SamFile_test.BasicTestBAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFetch) ... ok testTags (SamFile_test.BasicTestBAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFetch) ... ok testARcigar (SamFile_test.BasicTestBAMFile) ... ok testARcigarstring (SamFile_test.BasicTestBAMFile) ... ok testARflag (SamFile_test.BasicTestBAMFile) ... ok testARisize (SamFile_test.BasicTestBAMFile) ... ok testARmapq (SamFile_test.BasicTestBAMFile) ... ok testARmpos (SamFile_test.BasicTestBAMFile) ... ok testARmrnm (SamFile_test.BasicTestBAMFile) ... ok testARpos (SamFile_test.BasicTestBAMFile) ... ok testARqname (SamFile_test.BasicTestBAMFile) ... ok testARqqual (SamFile_test.BasicTestBAMFile) ... ok testARqual (SamFile_test.BasicTestBAMFile) ... ok testARquery (SamFile_test.BasicTestBAMFile) ... ok testARrname (SamFile_test.BasicTestBAMFile) ... ok testARseq (SamFile_test.BasicTestBAMFile) ... ok testAddTags (SamFile_test.BasicTestBAMFile) ... ok testAddTagsType (SamFile_test.BasicTestBAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFile) ... ok testMissingOpt (SamFile_test.BasicTestBAMFile) ... ok testOpt (SamFile_test.BasicTestBAMFile) ... ok testPairedBools (SamFile_test.BasicTestBAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFile) ... ok testTags (SamFile_test.BasicTestBAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFile) ... ok testARcigar (SamFile_test.BasicTestSAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestSAMFetch) ... ok testARflag (SamFile_test.BasicTestSAMFetch) ... ok testARisize (SamFile_test.BasicTestSAMFetch) ... ok testARmapq (SamFile_test.BasicTestSAMFetch) ... ok testARmpos (SamFile_test.BasicTestSAMFetch) ... ok testARmrnm (SamFile_test.BasicTestSAMFetch) ... ok testARpos (SamFile_test.BasicTestSAMFetch) ... ok testARqname (SamFile_test.BasicTestSAMFetch) ... ok testARqqual (SamFile_test.BasicTestSAMFetch) ... ok testARqual (SamFile_test.BasicTestSAMFetch) ... ok testARquery (SamFile_test.BasicTestSAMFetch) ... ok testARrname (SamFile_test.BasicTestSAMFetch) ... ok testARseq (SamFile_test.BasicTestSAMFetch) ... ok testAddTags (SamFile_test.BasicTestSAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestSAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestSAMFetch) ... ok testOpt (SamFile_test.BasicTestSAMFetch) ... ok testPairedBools (SamFile_test.BasicTestSAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFetch) ... ok testTags (SamFile_test.BasicTestSAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFetch) ... ok testARcigar (SamFile_test.BasicTestSAMFile) ... ok testARcigarstring (SamFile_test.BasicTestSAMFile) ... ok testARflag (SamFile_test.BasicTestSAMFile) ... ok testARisize (SamFile_test.BasicTestSAMFile) ... ok testARmapq (SamFile_test.BasicTestSAMFile) ... ok testARmpos (SamFile_test.BasicTestSAMFile) ... ok testARmrnm (SamFile_test.BasicTestSAMFile) ... ok testARpos (SamFile_test.BasicTestSAMFile) ... ok testARqname (SamFile_test.BasicTestSAMFile) ... ok testARqqual (SamFile_test.BasicTestSAMFile) ... ok testARqual (SamFile_test.BasicTestSAMFile) ... ok testARquery (SamFile_test.BasicTestSAMFile) ... ok testARrname (SamFile_test.BasicTestSAMFile) ... ok testARseq (SamFile_test.BasicTestSAMFile) ... ok testAddTags (SamFile_test.BasicTestSAMFile) ... ok testAddTagsType (SamFile_test.BasicTestSAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFile) ... ok testMissingOpt (SamFile_test.BasicTestSAMFile) ... ok testOpt (SamFile_test.BasicTestSAMFile) ... ok testPairedBools (SamFile_test.BasicTestSAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFile) ... ok testTags (SamFile_test.BasicTestSAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFile) ... ok testBlocks (SamFile_test.TestAlignedRead) ... ok testEmpty (SamFile_test.TestAlignedRead) ... ok build an example read. ... ok testPositions (SamFile_test.TestAlignedRead) ... ok testStrOfEmptyRead (SamFile_test.TestAlignedRead) ... ok test for tag parsing ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok testReadTags (SamFile_test.TestBTagBam) ... ok testReadWriteTags (SamFile_test.TestBTagBam) ... ok testReadTags (SamFile_test.TestBTagSam) ... ok testReadWriteTags (SamFile_test.TestBTagSam) ... ok testClipping (SamFile_test.TestClipping) ... ok testManager (SamFile_test.TestContextManager) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchUntilEOF (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchWithRegion (SamFile_test.TestDoubleFetch) ... ok testEmptyHeader (SamFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (SamFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (SamFile_test.TestExceptions) ... ok testBadContig (SamFile_test.TestExceptions) ... ok testMeaninglessCrap (SamFile_test.TestExceptions) ... ok testMissingFile (SamFile_test.TestExceptions) ... ok testOutOfRangNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (SamFile_test.TestExceptions) ... ok see issue 44 ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (SamFile_test.TestHeader1000Genomes) ... ok testHeaders (SamFile_test.TestHeaderBam) ... ok testNameMapping (SamFile_test.TestHeaderBam) ... ok testHeaders (SamFile_test.TestHeaderSam) ... ok testNameMapping (SamFile_test.TestHeaderSam) ... ok test if autodetection works. ... ok see issue 116 ... ok see issue 117 ... ok test that access to a closed samfile raises ValueError. ... ok testFetchFromClosedFile (SamFile_test.TestIO) ... ok test IteratorRowHead ... ok see issue 104. ... ok testReadSamWithoutHeader (SamFile_test.TestIO) ... ok see issue 104. ... ok testReadWriteBam (SamFile_test.TestIO) ... ok testReadWriteSamWithHeader (SamFile_test.TestIO) ... ok testReadWriteSamWithoutHeader (SamFile_test.TestIO) ... ok read from bam file without index. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok see issue 131 ... ok testStart (SamFile_test.TestIteratorColumn2) ... ok see issue 107. ... ok check random access per contig ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok when creating a read with a large entry in the tag field ... ok testBAM (SamFile_test.TestLargeOptValues) ... ok testSAM (SamFile_test.TestLargeOptValues) ... ok testFail1 (SamFile_test.TestLogging) ... ok testNoFail1 (SamFile_test.TestLogging) ... ok testNoFail2 (SamFile_test.TestLogging) ... ok testAllStepper (SamFile_test.TestPileup) ... ok testSamtoolsStepper (SamFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (SamFile_test.TestPileupObjects) ... ok testPileupRead (SamFile_test.TestPileupObjects) ... ok testFTPFetch (SamFile_test.TestRemoteFileFTP) ... ok testFTPView (SamFile_test.TestRemoteFileFTP) ... ok testFetch (SamFile_test.TestRemoteFileHTTP) ... ok testFetchAll (SamFile_test.TestRemoteFileHTTP) ... ok testView (SamFile_test.TestRemoteFileHTTP) ... ok testIndex (SamFile_test.TestSamfileIndex) ... ok testCount (SamFile_test.TestSamfileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok testIndex (SamFile_test.TestSamtoolsProxy) ... ok testSort (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testCigar (SamFile_test.TestTagParsing) ... ok testCigarString (SamFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (SamFile_test.TestTagParsing) ... ok testNegativeIntegers2 (SamFile_test.TestTagParsing) ... ok testBAM (SamFile_test.TestUnmappedReads) ... ok testOpenBamAsSam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (SamFile_test.TestWrongFormat) ... ok testOpenSamAsBam (SamFile_test.TestWrongFormat) ... ok test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... ok test_text_processing (StreamFiledescriptors_test.StreamTest) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok testIterator (VariantFile_test.TestHeader) ... ok testStr (VariantFile_test.TestHeader) ... ok testOpen (VariantFile_test.TestIndexFilename) ... ok testVCF (VariantFile_test.TestMissingGenotypes) ... ok testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok testDetectBCF (VariantFile_test.TestOpening) ... ok testDetectVCF (VariantFile_test.TestOpening) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testDetectVCFGZ (VariantFile_test.TestOpening) ... ok testEmptyFileVCF (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok testMissingFile (VariantFile_test.TestOpening) ... ok testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok testAlleles (VariantFile_test.TestParsing) ... ok testAlt (VariantFile_test.TestParsing) ... ok testChrom (VariantFile_test.TestParsing) ... ok testFilter (VariantFile_test.TestParsing) ... ok testFormat (VariantFile_test.TestParsing) ... ok testId (VariantFile_test.TestParsing) ... ok testInfo (VariantFile_test.TestParsing) ... ok testPos (VariantFile_test.TestParsing) ... ok testQual (VariantFile_test.TestParsing) ... ok testRef (VariantFile_test.TestParsing) ... ok testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok testSampleAlleles (VariantFile_test.TestParsing) ... ok testSampleFormats (VariantFile_test.TestParsing) ... ok testStart (VariantFile_test.TestParsing) ... ok testStop (VariantFile_test.TestParsing) ... ok testBase (VariantFile_test.TestSettingRecordValues) ... ok testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSubsetting (VariantFile_test.TestSubsetting) ... ok In file included from /<>/python-pysam-0.10.0+ds/tests/_compile_test.c:439:0: /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ testCount (compile_test.BAMTest) ... ok testCount (compile_test.GTFTest) ... ok testFetch (faidx_test.TestFastaFile) ... ok testFetchErrors (faidx_test.TestFastaFile) ... ok testLength (faidx_test.TestFastaFile) ... ok test out of range access. ... ok testSequenceLengths (faidx_test.TestFastaFile) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testCounts (faidx_test.TestFastqFileFastq) ... ok testManager (faidx_test.TestFastqFileFastq) ... ok testMissingFile (faidx_test.TestFastqFileFastq) ... ok testSequence (faidx_test.TestFastqFileFastq) ... ok testCounts (faidx_test.TestFastxFileFasta) ... ok testManager (faidx_test.TestFastxFileFasta) ... ok testMissingFile (faidx_test.TestFastxFileFasta) ... ok testSequence (faidx_test.TestFastxFileFasta) ... ok testCounts (faidx_test.TestFastxFileFastq) ... ok testManager (faidx_test.TestFastxFileFastq) ... ok testMissingFile (faidx_test.TestFastxFileFastq) ... ok testSequence (faidx_test.TestFastxFileFastq) ... ok testCounts (faidx_test.TestFastxFileFastqStream) ... ok testManager (faidx_test.TestFastxFileFastqStream) ... ok testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok testSequence (faidx_test.TestFastxFileFastqStream) ... ok testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok testFTPView (faidx_test.TestRemoteFileFTP) ... ok testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G ok testEmptyIndex (samtools_test.EmptyIndexTest) ... ok testStatements (samtools_test.PysamTest) ... ok testStatements (samtools_test.SamtoolsTest) ... ok testDoubleCalling (samtools_test.StdoutTest) ... ok testSaveStdout (samtools_test.StdoutTest) ... ok testWithRedirectedStdout (samtools_test.StdoutTest) ... ok testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok testReturnValueData (samtools_test.TestReturnType) ... ok testReturnValueString (samtools_test.TestReturnType) ... ok testBED (tabix_test.TestBackwardsCompatibility) ... ok testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok testEmpty (tabix_test.TestBackwardsCompatibility) ... ok testVCF (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok testRead (tabix_test.TestBed) ... ok testWrite (tabix_test.TestBed) ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok testManager (tabix_test.TestContextManager) ... ok testCopy (tabix_test.TestGTF) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestGTF) ... ok testSetting (tabix_test.TestGTF) ... ok testUnset (tabix_test.TestGTF) ... ok testWrite (tabix_test.TestGTF) ... ok testAll (tabix_test.TestGZFile) ... ok testFetchAll (tabix_test.TestIndexArgument) ... ok test indexing via preset. ... ok testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testAll (tabix_test.TestIterationWithComments) ... ok testGetContigs (tabix_test.TestIterationWithComments) ... ok testHeader (tabix_test.TestIterationWithComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok testPerContig (tabix_test.TestIterationWithComments) ... ok testPerContig2 (tabix_test.TestIterationWithComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok testPerInterval (tabix_test.TestIterationWithComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok testAll (tabix_test.TestIterationWithoutComments) ... ok testGetContigs (tabix_test.TestIterationWithoutComments) ... ok testHeader (tabix_test.TestIterationWithoutComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok testPerContig (tabix_test.TestIterationWithoutComments) ... ok testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok testPerInterval (tabix_test.TestIterationWithoutComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIterators) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileCompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok testDisjointIterators (tabix_test.TestMultipleIterators) ... ok testDoubleFetch (tabix_test.TestMultipleIterators) ... ok testJoinedIterators (tabix_test.TestMultipleIterators) ... ok testScope (tabix_test.TestMultipleIterators) ... ok testCopy (tabix_test.TestParser) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestParser) ... ok testUnset (tabix_test.TestParser) ... ok testWrite (tabix_test.TestParser) ... ok testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok testHeader (tabix_test.TestRemoteFileHTTP) ... ok testRead (tabix_test.TestVCFFromTabix) ... ok testWrite (tabix_test.TestVCFFromTabix) ... ok testConnecting (tabix_test.TestVCFFromVCF) ... ok testParsing (tabix_test.TestVCFFromVCF) ... ok testConnecting (tabix_test.TestVCFFromVariantFile) ... ok testParsing (tabix_test.TestVCFFromVariantFile) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok testParsing (tabix_test.TestVCFFromVariantFile_10) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok testParsing (tabix_test.TestVCFFromVariantFile_11) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok testParsing (tabix_test.TestVCFFromVariantFile_12) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok testParsing (tabix_test.TestVCFFromVariantFile_13) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok testParsing (tabix_test.TestVCFFromVariantFile_15) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_16) ... ok testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok testParsing (tabix_test.TestVCFFromVariantFile_18) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok testParsing (tabix_test.TestVCFFromVariantFile_2) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok testParsing (tabix_test.TestVCFFromVariantFile_22) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_24) ... ok testParsing (tabix_test.TestVCFFromVariantFile_24) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok testParsing (tabix_test.TestVCFFromVariantFile_4) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok testParsing (tabix_test.TestVCFFromVariantFile_6) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok testParsing (tabix_test.TestVCFFromVariantFile_7) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok testParsing (tabix_test.TestVCFFromVariantFile_8) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok testParsing (tabix_test.TestVCFFromVariantFile_9) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... ok testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testRead (tabix_test.VCFFromTabixTest_10) ... ok testWrite (tabix_test.VCFFromTabixTest_10) ... ok testRead (tabix_test.VCFFromTabixTest_11) ... ok testWrite (tabix_test.VCFFromTabixTest_11) ... ok testRead (tabix_test.VCFFromTabixTest_12) ... ok testWrite (tabix_test.VCFFromTabixTest_12) ... ok testRead (tabix_test.VCFFromTabixTest_13) ... ok testWrite (tabix_test.VCFFromTabixTest_13) ... ok testRead (tabix_test.VCFFromTabixTest_15) ... ok testWrite (tabix_test.VCFFromTabixTest_15) ... ok testRead (tabix_test.VCFFromTabixTest_16) ... ok testWrite (tabix_test.VCFFromTabixTest_16) ... ok testRead (tabix_test.VCFFromTabixTest_18) ... ok testWrite (tabix_test.VCFFromTabixTest_18) ... ok testRead (tabix_test.VCFFromTabixTest_2) ... ok testWrite (tabix_test.VCFFromTabixTest_2) ... ok testRead (tabix_test.VCFFromTabixTest_20) ... ok testWrite (tabix_test.VCFFromTabixTest_20) ... ok testRead (tabix_test.VCFFromTabixTest_21) ... ok testWrite (tabix_test.VCFFromTabixTest_21) ... ok testRead (tabix_test.VCFFromTabixTest_22) ... ok testWrite (tabix_test.VCFFromTabixTest_22) ... ok testRead (tabix_test.VCFFromTabixTest_23) ... ok testWrite (tabix_test.VCFFromTabixTest_23) ... ok testRead (tabix_test.VCFFromTabixTest_24) ... ok testWrite (tabix_test.VCFFromTabixTest_24) ... ok testRead (tabix_test.VCFFromTabixTest_3) ... ok testWrite (tabix_test.VCFFromTabixTest_3) ... ok testRead (tabix_test.VCFFromTabixTest_4) ... ok testWrite (tabix_test.VCFFromTabixTest_4) ... ok testRead (tabix_test.VCFFromTabixTest_5) ... ok testWrite (tabix_test.VCFFromTabixTest_5) ... ok testRead (tabix_test.VCFFromTabixTest_6) ... ok testWrite (tabix_test.VCFFromTabixTest_6) ... ok testRead (tabix_test.VCFFromTabixTest_7) ... ok testWrite (tabix_test.VCFFromTabixTest_7) ... ok testRead (tabix_test.VCFFromTabixTest_8) ... ok testWrite (tabix_test.VCFFromTabixTest_8) ... ok testRead (tabix_test.VCFFromTabixTest_9) ... ok testWrite (tabix_test.VCFFromTabixTest_9) ... ok testRead (tabix_test.VCFFromTabixTest_issue85) ... ok testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testConnecting (tabix_test.VCFFromVCFTest_10) ... ok testParsing (tabix_test.VCFFromVCFTest_10) ... ok testConnecting (tabix_test.VCFFromVCFTest_11) ... ok testParsing (tabix_test.VCFFromVCFTest_11) ... ok testConnecting (tabix_test.VCFFromVCFTest_12) ... ok testParsing (tabix_test.VCFFromVCFTest_12) ... ok testConnecting (tabix_test.VCFFromVCFTest_13) ... ok testParsing (tabix_test.VCFFromVCFTest_13) ... ok testConnecting (tabix_test.VCFFromVCFTest_15) ... ok testParsing (tabix_test.VCFFromVCFTest_15) ... ok testConnecting (tabix_test.VCFFromVCFTest_16) ... ok testParsing (tabix_test.VCFFromVCFTest_16) ... ok testConnecting (tabix_test.VCFFromVCFTest_18) ... ok testParsing (tabix_test.VCFFromVCFTest_18) ... ok testConnecting (tabix_test.VCFFromVCFTest_2) ... ok testParsing (tabix_test.VCFFromVCFTest_2) ... ok testConnecting (tabix_test.VCFFromVCFTest_20) ... ok testParsing (tabix_test.VCFFromVCFTest_20) ... ok testConnecting (tabix_test.VCFFromVCFTest_21) ... ok testParsing (tabix_test.VCFFromVCFTest_21) ... ok testConnecting (tabix_test.VCFFromVCFTest_22) ... ok testParsing (tabix_test.VCFFromVCFTest_22) ... ok testConnecting (tabix_test.VCFFromVCFTest_23) ... ok testParsing (tabix_test.VCFFromVCFTest_23) ... ok testConnecting (tabix_test.VCFFromVCFTest_24) ... ok testParsing (tabix_test.VCFFromVCFTest_24) ... ok testConnecting (tabix_test.VCFFromVCFTest_3) ... ok testParsing (tabix_test.VCFFromVCFTest_3) ... ok testConnecting (tabix_test.VCFFromVCFTest_4) ... ok testParsing (tabix_test.VCFFromVCFTest_4) ... ok testConnecting (tabix_test.VCFFromVCFTest_5) ... ok testParsing (tabix_test.VCFFromVCFTest_5) ... ok testConnecting (tabix_test.VCFFromVCFTest_6) ... ok testParsing (tabix_test.VCFFromVCFTest_6) ... ok testConnecting (tabix_test.VCFFromVCFTest_7) ... ok testParsing (tabix_test.VCFFromVCFTest_7) ... ok testConnecting (tabix_test.VCFFromVCFTest_8) ... ok testParsing (tabix_test.VCFFromVCFTest_8) ... ok testConnecting (tabix_test.VCFFromVCFTest_9) ... ok testParsing (tabix_test.VCFFromVCFTest_9) ... ok testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok test_samtools_python.test_idxstats_parse_split_lines ... ok test_samtools_python.test_bedcov_split_lines ... ok test_samtools_python.test_idxstats_parse ... ok test_samtools_python.test_bedcov ... ok ---------------------------------------------------------------------- Ran 916 tests in 104.440s OK (0, 0) I: pybuild base:184: cd /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose reference bases should always be the same nucleotide ... ok testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok check comparison functions. ... ok testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok see issue 26 ... ok testHashing (AlignedSegment_test.TestAlignedSegment) ... ok build an example read. ... ok issue 176: retrieving length without query sequence ... ok testPositions (AlignedSegment_test.TestAlignedSegment) ... ok see issue 62 ... ok testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok testAsString (AlignedSegment_test.TestAsString) ... ok testStats (AlignedSegment_test.TestCigarStats) ... ok testCopy (AlignedSegment_test.TestCopy) ... ok testDeepCopy (AlignedSegment_test.TestCopy) ... ok testAddTags (AlignedSegment_test.TestTags) ... ok testAddTagsType (AlignedSegment_test.TestTags) ... ok testArrayTags (AlignedSegment_test.TestTags) ... ok testEmptyTag (AlignedSegment_test.TestTags) ... ok testMDTagComplex (AlignedSegment_test.TestTags) ... ok testMDTagDeletions (AlignedSegment_test.TestTags) ... ok testMDTagInsertions (AlignedSegment_test.TestTags) ... ok testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok testMissingTag (AlignedSegment_test.TestTags) ... ok testSetTag (AlignedSegment_test.TestTags) ... ok test for tag parsing ... ok testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok test BAM autodetection. ... ok test CRAM autodetection. ... ok test SAM autodetection. ... ok testReadTags (AlignmentFile_test.TestBTagBam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok testReadTags (AlignmentFile_test.TestBTagSam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok testClipping (AlignmentFile_test.TestClipping) ... ok testManager (AlignmentFile_test.TestContextManager) ... ok test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok testBadContig (AlignmentFile_test.TestExceptions) ... ok testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok testMissingFile (AlignmentFile_test.TestExceptions) ... ok testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok see issue 44 ... ok testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<>/python-pysam-0.10.0+ds/tests/pysam_data/ex1.bam.bai ok testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok test_all (AlignmentFile_test.TestFindIntrons) ... ok test_first (AlignmentFile_test.TestFindIntrons) ... ok test_total (AlignmentFile_test.TestFindIntrons) ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok testBAM2BAM (AlignmentFile_test.TestIO) ... ok testBAM2CRAM (AlignmentFile_test.TestIO) ... ok testBAM2SAM (AlignmentFile_test.TestIO) ... ok see issue 116 ... ok see issue 116 ... ok see issue 117 ... ok testCRAM2BAM (AlignmentFile_test.TestIO) ... ok testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok testCRAM2SAM (AlignmentFile_test.TestIO) ... ok test that access to a closed samfile raises ValueError. ... ok testEmptyBAM (AlignmentFile_test.TestIO) ... ok testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok test IteratorRowHead ... ok testOpenFromFilename (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok testReadSamWithoutHeader (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok read from bam file without index. ... ok testSAM2BAM (AlignmentFile_test.TestIO) ... ok testSAM2CRAM (AlignmentFile_test.TestIO) ... ok testSAM2SAM (AlignmentFile_test.TestIO) ... ok testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok read from uncompressed BAM file, see issue #43 ... ok see issue 131 ... ok testStart (AlignmentFile_test.TestIteratorColumn2) ... ok test if PileupRead can be printed. ... ok see issue 107. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok when creating a read with a large entry in the tag field ... ok testBAM (AlignmentFile_test.TestLargeOptValues) ... ok testSAM (AlignmentFile_test.TestLargeOptValues) ... ok testFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail2 (AlignmentFile_test.TestLogging) ... ok testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok testAllStepper (AlignmentFile_test.TestPileup) ... ok testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok testArrayTags (AlignmentFile_test.TestTagParsing) ... ok testCigar (AlignmentFile_test.TestTagParsing) ... ok testCigarString (AlignmentFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok testTruncatedBam (AlignmentFile_test.TestTruncatedBAM) ... [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes ok See comments for pull request at ... ok testBAM (AlignmentFile_test.TestUnmappedReads) ... ok testVerbosity (AlignmentFile_test.TestVerbosity) ... ok testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok testARcigar (SamFile_test.BasicTestBAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestBAMFetch) ... ok testARflag (SamFile_test.BasicTestBAMFetch) ... ok testARisize (SamFile_test.BasicTestBAMFetch) ... ok testARmapq (SamFile_test.BasicTestBAMFetch) ... ok testARmpos (SamFile_test.BasicTestBAMFetch) ... ok testARmrnm (SamFile_test.BasicTestBAMFetch) ... ok testARpos (SamFile_test.BasicTestBAMFetch) ... ok testARqname (SamFile_test.BasicTestBAMFetch) ... ok testARqqual (SamFile_test.BasicTestBAMFetch) ... ok testARqual (SamFile_test.BasicTestBAMFetch) ... ok testARquery (SamFile_test.BasicTestBAMFetch) ... ok testARrname (SamFile_test.BasicTestBAMFetch) ... ok testARseq (SamFile_test.BasicTestBAMFetch) ... ok testAddTags (SamFile_test.BasicTestBAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestBAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestBAMFetch) ... ok testOpt (SamFile_test.BasicTestBAMFetch) ... ok testPairedBools (SamFile_test.BasicTestBAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFetch) ... ok testTags (SamFile_test.BasicTestBAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFetch) ... ok testARcigar (SamFile_test.BasicTestBAMFile) ... ok testARcigarstring (SamFile_test.BasicTestBAMFile) ... ok testARflag (SamFile_test.BasicTestBAMFile) ... ok testARisize (SamFile_test.BasicTestBAMFile) ... ok testARmapq (SamFile_test.BasicTestBAMFile) ... ok testARmpos (SamFile_test.BasicTestBAMFile) ... ok testARmrnm (SamFile_test.BasicTestBAMFile) ... ok testARpos (SamFile_test.BasicTestBAMFile) ... ok testARqname (SamFile_test.BasicTestBAMFile) ... ok testARqqual (SamFile_test.BasicTestBAMFile) ... ok testARqual (SamFile_test.BasicTestBAMFile) ... ok testARquery (SamFile_test.BasicTestBAMFile) ... ok testARrname (SamFile_test.BasicTestBAMFile) ... ok testARseq (SamFile_test.BasicTestBAMFile) ... ok testAddTags (SamFile_test.BasicTestBAMFile) ... ok testAddTagsType (SamFile_test.BasicTestBAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFile) ... ok testMissingOpt (SamFile_test.BasicTestBAMFile) ... ok testOpt (SamFile_test.BasicTestBAMFile) ... ok testPairedBools (SamFile_test.BasicTestBAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFile) ... ok testTags (SamFile_test.BasicTestBAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFile) ... ok testARcigar (SamFile_test.BasicTestSAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestSAMFetch) ... ok testARflag (SamFile_test.BasicTestSAMFetch) ... ok testARisize (SamFile_test.BasicTestSAMFetch) ... ok testARmapq (SamFile_test.BasicTestSAMFetch) ... ok testARmpos (SamFile_test.BasicTestSAMFetch) ... ok testARmrnm (SamFile_test.BasicTestSAMFetch) ... ok testARpos (SamFile_test.BasicTestSAMFetch) ... ok testARqname (SamFile_test.BasicTestSAMFetch) ... ok testARqqual (SamFile_test.BasicTestSAMFetch) ... ok testARqual (SamFile_test.BasicTestSAMFetch) ... ok testARquery (SamFile_test.BasicTestSAMFetch) ... ok testARrname (SamFile_test.BasicTestSAMFetch) ... ok testARseq (SamFile_test.BasicTestSAMFetch) ... ok testAddTags (SamFile_test.BasicTestSAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestSAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestSAMFetch) ... ok testOpt (SamFile_test.BasicTestSAMFetch) ... ok testPairedBools (SamFile_test.BasicTestSAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFetch) ... ok testTags (SamFile_test.BasicTestSAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFetch) ... ok testARcigar (SamFile_test.BasicTestSAMFile) ... ok testARcigarstring (SamFile_test.BasicTestSAMFile) ... ok testARflag (SamFile_test.BasicTestSAMFile) ... ok testARisize (SamFile_test.BasicTestSAMFile) ... ok testARmapq (SamFile_test.BasicTestSAMFile) ... ok testARmpos (SamFile_test.BasicTestSAMFile) ... ok testARmrnm (SamFile_test.BasicTestSAMFile) ... ok testARpos (SamFile_test.BasicTestSAMFile) ... ok testARqname (SamFile_test.BasicTestSAMFile) ... ok testARqqual (SamFile_test.BasicTestSAMFile) ... ok testARqual (SamFile_test.BasicTestSAMFile) ... ok testARquery (SamFile_test.BasicTestSAMFile) ... ok testARrname (SamFile_test.BasicTestSAMFile) ... ok testARseq (SamFile_test.BasicTestSAMFile) ... ok testAddTags (SamFile_test.BasicTestSAMFile) ... ok testAddTagsType (SamFile_test.BasicTestSAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFile) ... ok testMissingOpt (SamFile_test.BasicTestSAMFile) ... ok testOpt (SamFile_test.BasicTestSAMFile) ... ok testPairedBools (SamFile_test.BasicTestSAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFile) ... ok testTags (SamFile_test.BasicTestSAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFile) ... ok testBlocks (SamFile_test.TestAlignedRead) ... ok testEmpty (SamFile_test.TestAlignedRead) ... ok build an example read. ... ok testPositions (SamFile_test.TestAlignedRead) ... ok testStrOfEmptyRead (SamFile_test.TestAlignedRead) ... ok test for tag parsing ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok testReadTags (SamFile_test.TestBTagBam) ... ok testReadWriteTags (SamFile_test.TestBTagBam) ... ok testReadTags (SamFile_test.TestBTagSam) ... ok testReadWriteTags (SamFile_test.TestBTagSam) ... ok testClipping (SamFile_test.TestClipping) ... ok testManager (SamFile_test.TestContextManager) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchUntilEOF (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchWithRegion (SamFile_test.TestDoubleFetch) ... ok testEmptyHeader (SamFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (SamFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (SamFile_test.TestExceptions) ... ok testBadContig (SamFile_test.TestExceptions) ... ok testMeaninglessCrap (SamFile_test.TestExceptions) ... ok testMissingFile (SamFile_test.TestExceptions) ... ok testOutOfRangNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (SamFile_test.TestExceptions) ... ok see issue 44 ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (SamFile_test.TestHeader1000Genomes) ... ok testHeaders (SamFile_test.TestHeaderBam) ... ok testNameMapping (SamFile_test.TestHeaderBam) ... ok testHeaders (SamFile_test.TestHeaderSam) ... ok testNameMapping (SamFile_test.TestHeaderSam) ... ok test if autodetection works. ... ok see issue 116 ... ok see issue 117 ... ok test that access to a closed samfile raises ValueError. ... ok testFetchFromClosedFile (SamFile_test.TestIO) ... ok test IteratorRowHead ... ok see issue 104. ... ok testReadSamWithoutHeader (SamFile_test.TestIO) ... ok see issue 104. ... ok testReadWriteBam (SamFile_test.TestIO) ... ok testReadWriteSamWithHeader (SamFile_test.TestIO) ... ok testReadWriteSamWithoutHeader (SamFile_test.TestIO) ... ok read from bam file without index. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok see issue 131 ... ok testStart (SamFile_test.TestIteratorColumn2) ... ok see issue 107. ... ok check random access per contig ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok when creating a read with a large entry in the tag field ... ok testBAM (SamFile_test.TestLargeOptValues) ... ok testSAM (SamFile_test.TestLargeOptValues) ... ok testFail1 (SamFile_test.TestLogging) ... ok testNoFail1 (SamFile_test.TestLogging) ... ok testNoFail2 (SamFile_test.TestLogging) ... ok testAllStepper (SamFile_test.TestPileup) ... ok testSamtoolsStepper (SamFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (SamFile_test.TestPileupObjects) ... ok testPileupRead (SamFile_test.TestPileupObjects) ... ok testFTPFetch (SamFile_test.TestRemoteFileFTP) ... ok testFTPView (SamFile_test.TestRemoteFileFTP) ... ok testFetch (SamFile_test.TestRemoteFileHTTP) ... ok testFetchAll (SamFile_test.TestRemoteFileHTTP) ... ok testView (SamFile_test.TestRemoteFileHTTP) ... ok testIndex (SamFile_test.TestSamfileIndex) ... ok testCount (SamFile_test.TestSamfileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok testIndex (SamFile_test.TestSamtoolsProxy) ... ok testSort (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testCigar (SamFile_test.TestTagParsing) ... ok testCigarString (SamFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (SamFile_test.TestTagParsing) ... ok testNegativeIntegers2 (SamFile_test.TestTagParsing) ... ok testBAM (SamFile_test.TestUnmappedReads) ... ok testOpenBamAsSam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (SamFile_test.TestWrongFormat) ... ok testOpenSamAsBam (SamFile_test.TestWrongFormat) ... ok test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... ok test_text_processing (StreamFiledescriptors_test.StreamTest) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok testIterator (VariantFile_test.TestHeader) ... ok testStr (VariantFile_test.TestHeader) ... ok testOpen (VariantFile_test.TestIndexFilename) ... ok testVCF (VariantFile_test.TestMissingGenotypes) ... ok testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok testDetectBCF (VariantFile_test.TestOpening) ... ok testDetectVCF (VariantFile_test.TestOpening) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testDetectVCFGZ (VariantFile_test.TestOpening) ... ok testEmptyFileVCF (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok testMissingFile (VariantFile_test.TestOpening) ... ok testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok testAlleles (VariantFile_test.TestParsing) ... ok testAlt (VariantFile_test.TestParsing) ... ok testChrom (VariantFile_test.TestParsing) ... ok testFilter (VariantFile_test.TestParsing) ... ok testFormat (VariantFile_test.TestParsing) ... ok testId (VariantFile_test.TestParsing) ... ok testInfo (VariantFile_test.TestParsing) ... ok testPos (VariantFile_test.TestParsing) ... ok testQual (VariantFile_test.TestParsing) ... ok testRef (VariantFile_test.TestParsing) ... ok testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok testSampleAlleles (VariantFile_test.TestParsing) ... ok testSampleFormats (VariantFile_test.TestParsing) ... ok testStart (VariantFile_test.TestParsing) ... ok testStop (VariantFile_test.TestParsing) ... ok testBase (VariantFile_test.TestSettingRecordValues) ... ok testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSubsetting (VariantFile_test.TestSubsetting) ... In file included from /<>/python-pysam-0.10.0+ds/tests/_compile_test.c:439:0: /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ ok testCount (compile_test.BAMTest) ... ok testCount (compile_test.GTFTest) ... ok testFetch (faidx_test.TestFastaFile) ... ok testFetchErrors (faidx_test.TestFastaFile) ... ok testLength (faidx_test.TestFastaFile) ... ok test out of range access. ... ok testSequenceLengths (faidx_test.TestFastaFile) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testCounts (faidx_test.TestFastqFileFastq) ... ok testManager (faidx_test.TestFastqFileFastq) ... ok testMissingFile (faidx_test.TestFastqFileFastq) ... ok testSequence (faidx_test.TestFastqFileFastq) ... ok testCounts (faidx_test.TestFastxFileFasta) ... ok testManager (faidx_test.TestFastxFileFasta) ... ok testMissingFile (faidx_test.TestFastxFileFasta) ... ok testSequence (faidx_test.TestFastxFileFasta) ... ok testCounts (faidx_test.TestFastxFileFastq) ... ok testManager (faidx_test.TestFastxFileFastq) ... ok testMissingFile (faidx_test.TestFastxFileFastq) ... ok testSequence (faidx_test.TestFastxFileFastq) ... ok testCounts (faidx_test.TestFastxFileFastqStream) ... ok testManager (faidx_test.TestFastxFileFastqStream) ... ok testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok testSequence (faidx_test.TestFastxFileFastqStream) ... ok testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok testFTPView (faidx_test.TestRemoteFileFTP) ... ok testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G ok testEmptyIndex (samtools_test.EmptyIndexTest) ... ok testStatements (samtools_test.PysamTest) ... ok testStatements (samtools_test.SamtoolsTest) ... ok testDoubleCalling (samtools_test.StdoutTest) ... ok testSaveStdout (samtools_test.StdoutTest) ... ok testWithRedirectedStdout (samtools_test.StdoutTest) ... ok testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok testReturnValueData (samtools_test.TestReturnType) ... ok testReturnValueString (samtools_test.TestReturnType) ... ok testBED (tabix_test.TestBackwardsCompatibility) ... ok testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok testEmpty (tabix_test.TestBackwardsCompatibility) ... ok testVCF (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok testRead (tabix_test.TestBed) ... ok testWrite (tabix_test.TestBed) ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok testManager (tabix_test.TestContextManager) ... ok testCopy (tabix_test.TestGTF) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestGTF) ... ok testSetting (tabix_test.TestGTF) ... ok testUnset (tabix_test.TestGTF) ... ok testWrite (tabix_test.TestGTF) ... ok testAll (tabix_test.TestGZFile) ... ok testFetchAll (tabix_test.TestIndexArgument) ... ok test indexing via preset. ... ok testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testAll (tabix_test.TestIterationWithComments) ... ok testGetContigs (tabix_test.TestIterationWithComments) ... ok testHeader (tabix_test.TestIterationWithComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok testPerContig (tabix_test.TestIterationWithComments) ... ok testPerContig2 (tabix_test.TestIterationWithComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok testPerInterval (tabix_test.TestIterationWithComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok testAll (tabix_test.TestIterationWithoutComments) ... ok testGetContigs (tabix_test.TestIterationWithoutComments) ... ok testHeader (tabix_test.TestIterationWithoutComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok testPerContig (tabix_test.TestIterationWithoutComments) ... ok testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok testPerInterval (tabix_test.TestIterationWithoutComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIterators) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileCompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok testDisjointIterators (tabix_test.TestMultipleIterators) ... ok testDoubleFetch (tabix_test.TestMultipleIterators) ... ok testJoinedIterators (tabix_test.TestMultipleIterators) ... ok testScope (tabix_test.TestMultipleIterators) ... ok testCopy (tabix_test.TestParser) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestParser) ... ok testUnset (tabix_test.TestParser) ... ok testWrite (tabix_test.TestParser) ... ok testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok testHeader (tabix_test.TestRemoteFileHTTP) ... ok testFromTabix (tabix_test.TestUnicode) ... ok testFromVCF (tabix_test.TestUnicode) ... ok testRead (tabix_test.TestVCFFromTabix) ... ok testWrite (tabix_test.TestVCFFromTabix) ... ok testConnecting (tabix_test.TestVCFFromVCF) ... ok testParsing (tabix_test.TestVCFFromVCF) ... ok testConnecting (tabix_test.TestVCFFromVariantFile) ... ok testParsing (tabix_test.TestVCFFromVariantFile) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok testParsing (tabix_test.TestVCFFromVariantFile_10) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok testParsing (tabix_test.TestVCFFromVariantFile_11) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok testParsing (tabix_test.TestVCFFromVariantFile_12) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok testParsing (tabix_test.TestVCFFromVariantFile_13) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok testParsing (tabix_test.TestVCFFromVariantFile_15) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_16) ... ok testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok testParsing (tabix_test.TestVCFFromVariantFile_18) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok testParsing (tabix_test.TestVCFFromVariantFile_2) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok testParsing (tabix_test.TestVCFFromVariantFile_22) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_24) ... ok testParsing (tabix_test.TestVCFFromVariantFile_24) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok testParsing (tabix_test.TestVCFFromVariantFile_4) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok testParsing (tabix_test.TestVCFFromVariantFile_6) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok testParsing (tabix_test.TestVCFFromVariantFile_7) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok testParsing (tabix_test.TestVCFFromVariantFile_8) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok testParsing (tabix_test.TestVCFFromVariantFile_9) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... ok testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testRead (tabix_test.VCFFromTabixTest_10) ... ok testWrite (tabix_test.VCFFromTabixTest_10) ... ok testRead (tabix_test.VCFFromTabixTest_11) ... ok testWrite (tabix_test.VCFFromTabixTest_11) ... ok testRead (tabix_test.VCFFromTabixTest_12) ... ok testWrite (tabix_test.VCFFromTabixTest_12) ... ok testRead (tabix_test.VCFFromTabixTest_13) ... ok testWrite (tabix_test.VCFFromTabixTest_13) ... ok testRead (tabix_test.VCFFromTabixTest_15) ... ok testWrite (tabix_test.VCFFromTabixTest_15) ... ok testRead (tabix_test.VCFFromTabixTest_16) ... ok testWrite (tabix_test.VCFFromTabixTest_16) ... ok testRead (tabix_test.VCFFromTabixTest_18) ... ok testWrite (tabix_test.VCFFromTabixTest_18) ... ok testRead (tabix_test.VCFFromTabixTest_2) ... ok testWrite (tabix_test.VCFFromTabixTest_2) ... ok testRead (tabix_test.VCFFromTabixTest_20) ... ok testWrite (tabix_test.VCFFromTabixTest_20) ... ok testRead (tabix_test.VCFFromTabixTest_21) ... ok testWrite (tabix_test.VCFFromTabixTest_21) ... ok testRead (tabix_test.VCFFromTabixTest_22) ... ok testWrite (tabix_test.VCFFromTabixTest_22) ... ok testRead (tabix_test.VCFFromTabixTest_23) ... ok testWrite (tabix_test.VCFFromTabixTest_23) ... ok testRead (tabix_test.VCFFromTabixTest_24) ... ok testWrite (tabix_test.VCFFromTabixTest_24) ... ok testRead (tabix_test.VCFFromTabixTest_3) ... ok testWrite (tabix_test.VCFFromTabixTest_3) ... ok testRead (tabix_test.VCFFromTabixTest_4) ... ok testWrite (tabix_test.VCFFromTabixTest_4) ... ok testRead (tabix_test.VCFFromTabixTest_5) ... ok testWrite (tabix_test.VCFFromTabixTest_5) ... ok testRead (tabix_test.VCFFromTabixTest_6) ... ok testWrite (tabix_test.VCFFromTabixTest_6) ... ok testRead (tabix_test.VCFFromTabixTest_7) ... ok testWrite (tabix_test.VCFFromTabixTest_7) ... ok testRead (tabix_test.VCFFromTabixTest_8) ... ok testWrite (tabix_test.VCFFromTabixTest_8) ... ok testRead (tabix_test.VCFFromTabixTest_9) ... ok testWrite (tabix_test.VCFFromTabixTest_9) ... ok testRead (tabix_test.VCFFromTabixTest_issue85) ... ok testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testConnecting (tabix_test.VCFFromVCFTest_10) ... ok testParsing (tabix_test.VCFFromVCFTest_10) ... ok testConnecting (tabix_test.VCFFromVCFTest_11) ... ok testParsing (tabix_test.VCFFromVCFTest_11) ... ok testConnecting (tabix_test.VCFFromVCFTest_12) ... ok testParsing (tabix_test.VCFFromVCFTest_12) ... ok testConnecting (tabix_test.VCFFromVCFTest_13) ... ok testParsing (tabix_test.VCFFromVCFTest_13) ... ok testConnecting (tabix_test.VCFFromVCFTest_15) ... ok testParsing (tabix_test.VCFFromVCFTest_15) ... ok testConnecting (tabix_test.VCFFromVCFTest_16) ... ok testParsing (tabix_test.VCFFromVCFTest_16) ... ok testConnecting (tabix_test.VCFFromVCFTest_18) ... ok testParsing (tabix_test.VCFFromVCFTest_18) ... ok testConnecting (tabix_test.VCFFromVCFTest_2) ... ok testParsing (tabix_test.VCFFromVCFTest_2) ... ok testConnecting (tabix_test.VCFFromVCFTest_20) ... ok testParsing (tabix_test.VCFFromVCFTest_20) ... ok testConnecting (tabix_test.VCFFromVCFTest_21) ... ok testParsing (tabix_test.VCFFromVCFTest_21) ... ok testConnecting (tabix_test.VCFFromVCFTest_22) ... ok testParsing (tabix_test.VCFFromVCFTest_22) ... ok testConnecting (tabix_test.VCFFromVCFTest_23) ... ok testParsing (tabix_test.VCFFromVCFTest_23) ... ok testConnecting (tabix_test.VCFFromVCFTest_24) ... ok testParsing (tabix_test.VCFFromVCFTest_24) ... ok testConnecting (tabix_test.VCFFromVCFTest_3) ... ok testParsing (tabix_test.VCFFromVCFTest_3) ... ok testConnecting (tabix_test.VCFFromVCFTest_4) ... ok testParsing (tabix_test.VCFFromVCFTest_4) ... ok testConnecting (tabix_test.VCFFromVCFTest_5) ... ok testParsing (tabix_test.VCFFromVCFTest_5) ... ok testConnecting (tabix_test.VCFFromVCFTest_6) ... ok testParsing (tabix_test.VCFFromVCFTest_6) ... ok testConnecting (tabix_test.VCFFromVCFTest_7) ... ok testParsing (tabix_test.VCFFromVCFTest_7) ... ok testConnecting (tabix_test.VCFFromVCFTest_8) ... ok testParsing (tabix_test.VCFFromVCFTest_8) ... ok testConnecting (tabix_test.VCFFromVCFTest_9) ... ok testParsing (tabix_test.VCFFromVCFTest_9) ... ok testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok test_samtools_python.test_idxstats_parse_split_lines ... ok test_samtools_python.test_bedcov_split_lines ... ok test_samtools_python.test_idxstats_parse ... ok test_samtools_python.test_bedcov ... ok ---------------------------------------------------------------------- Ran 918 tests in 107.421s OK (0, 0) make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' fakeroot debian/rules binary dh binary --with python2,python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py install --root /<>/python-pysam-0.10.0+ds/debian/python-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7 creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/namedtuple.py to namedtuple.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/c*.pxd' warning: no files found matching 'pysam/c*.pyx' warning: no files found matching 'pysam/c*.c' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:184: /usr/bin/python3 setup.py install --root /<>/python-pysam-0.10.0+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5 creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/__init__.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/config.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/samtools.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/bcftools.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/version.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/Pileup.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/utils.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-x86_64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/utils.py to utils.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/config.py to config.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/__init__.py to __init__.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/version.py to version.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/bcftools.py to bcftools.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/samtools.py to samtools.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/namedtuple.py to namedtuple.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/Pileup.py to Pileup.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__init__.py to __init__.cpython-35.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/c*.pxd' warning: no files found matching 'pysam/c*.pyx' warning: no files found matching 'pysam/c*.c' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam-0.10.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c dh_install -Xtest.gtf.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 fs:322: renaming libcalignedsegment.so to libcalignedsegment.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcalignmentfile.so to libcalignmentfile.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcbcf.so to libcbcf.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcbgzf.so to libcbgzf.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcfaidx.so to libcfaidx.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libchtslib.so to libchtslib.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcsamfile.so to libcsamfile.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libctabix.so to libctabix.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libctabixproxies.so to libctabixproxies.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcutils.so to libcutils.x86_64-linux-gnu.so I: dh_python2 fs:322: renaming libcvcf.so to libcvcf.x86_64-linux-gnu.so dh_python3 -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: python-pysam python3-pysam dh_strip debug symbol extraction: packages to act on: python-pysam python3-pysam dh_strip debug symbol extraction: ignored packages: /usr/bin/pkg_create_dbgsym: ignoring python* package: python-pysam /usr/bin/pkg_create_dbgsym: ignoring python* package: python3-pysam dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform amd64: python-pysam python3-pysam dh_gencontrol debug symbol wrapper: packages to act on: python-pysam python3-pysam dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/python-pysam-dbgsym, skipping package python-pysam dh_gencontrol debug symbol wrapper: no debian/python3-pysam-dbgsym, skipping package python3-pysam dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python-pysam-tests (in debian/python-pysam-tests); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/python-pysam-tests/DEBIAN/control, package python-pysam-tests, directory debian/python-pysam-tests INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... pkgstripfiles: processing control file: debian/python-pysam/DEBIAN/control, package python-pysam, directory debian/python-pysam pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam' in '../python-pysam_0.10.0+ds-1ubuntu1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.10.0+ds-1ubuntu1_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/python-pysam-tests/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-tests ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.10.0+ds-1ubuntu1_all.deb'. dpkg-genchanges --build=any,all -mLaunchpad Build Daemon >../python-pysam_0.10.0+ds-1ubuntu1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build python-pysam-0.10.0+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170127-0951 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.10.0+ds-1ubuntu1_amd64.changes: ---------------------------------------------- Format: 1.8 Date: Fri, 27 Jan 2017 11:27:10 +0200 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: all amd64 Version: 0.10.0+ds-1ubuntu1 Distribution: zesty-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.10.0+ds-1ubuntu1) zesty; urgency=medium . * Disable PIE for building a Python extension Checksums-Sha1: 4a07ab0dadb152d8738e5c34f8d3a1458caebde7 855368 python-pysam-tests_0.10.0+ds-1ubuntu1_all.deb d082e3bb3d161a5b82d1d3158d85012fe54ba86c 1300000 python-pysam_0.10.0+ds-1ubuntu1_amd64.deb e9cb45124ccaf61edde862c886f83142f68cf1c7 1297868 python3-pysam_0.10.0+ds-1ubuntu1_amd64.deb Checksums-Sha256: 4c54fc2014ce43b64705ff7657f1be11ad4a73fa9e52f1cba1c7c3602bb45498 855368 python-pysam-tests_0.10.0+ds-1ubuntu1_all.deb a0b6e31524b8e68db2d3ecb9d0a855ca8d89e044c7dd1d2c4d3c0e8eea996b4d 1300000 python-pysam_0.10.0+ds-1ubuntu1_amd64.deb 57effd657d3ddb9367c73dccecb0c74df71767a9471b48efc586b851530355ea 1297868 python3-pysam_0.10.0+ds-1ubuntu1_amd64.deb Files: 1966ea38e086bdcf814dc452962a2a11 855368 python optional python-pysam-tests_0.10.0+ds-1ubuntu1_all.deb 0cc085758b614462dd4a88500b966a43 1300000 python optional python-pysam_0.10.0+ds-1ubuntu1_amd64.deb 54a325351234771c0031526d41c83cf9 1297868 python optional python3-pysam_0.10.0+ds-1ubuntu1_amd64.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam-tests_0.10.0+ds-1ubuntu1_all.deb --------------------------------------------- new debian package, version 2.0. size 855368 bytes: control archive=3924 bytes. 723 bytes, 18 lines control 12171 bytes, 129 lines md5sums Package: python-pysam-tests Source: python-pysam Version: 0.10.0+ds-1ubuntu1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 1003 Enhances: python-pysam Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (test data) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package contains the data provided by upstream to run the pysam test suite. 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python-pysam Version: 0.10.0+ds-1ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 4428 Depends: libc6 (>= 2.14), libhts1 (>= 1.3), zlib1g (>= 1:1.1.4), python (<< 2.8), python (>= 2.7~), python:any (<< 2.8), python:any (>= 2.7.5-5~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 2. 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1:1.1.4), python3 (<< 3.6), python3 (>= 3.5~), python3:any (>= 3.3.2-2~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 3. 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./usr/share/ drwxr-xr-x root/root 0 2017-01-27 09:27 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-01-27 09:27 ./usr/share/doc/python3-pysam/ -rw-r--r-- root/root 1959 2017-01-27 09:27 ./usr/share/doc/python3-pysam/changelog.Debian.gz -rw-r--r-- root/root 6835 2016-04-09 22:12 ./usr/share/doc/python3-pysam/copyright drwxr-xr-x root/root 0 2017-01-27 09:27 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-01-27 09:27 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 209 2017-01-26 05:32 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 151372 Build-Time: 599 Distribution: zesty-proposed Host Architecture: amd64 Install-Time: 43 Job: python-pysam_0.10.0+ds-1ubuntu1.dsc Machine Architecture: amd64 Package: python-pysam Package-Time: 643 Source-Version: 0.10.0+ds-1ubuntu1 Space: 151372 Status: successful Version: 0.10.0+ds-1ubuntu1 -------------------------------------------------------------------------------- Finished at 20170127-0951 Build needed 00:10:43, 151372k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11930830'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11930830/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11930830'] Unmounting chroot for build PACKAGEBUILD-11930830... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11930830'] Removing build PACKAGEBUILD-11930830