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So we exec the FD to /dev/null, -# effectively closing config.log, so it can be properly (re)opened and -# appended to by config.status. When coming back to configure, we -# need to make the FD available again. -if test "$no_create" != yes; then - ac_cs_success=: - ac_config_status_args= - test "$silent" = yes && - ac_config_status_args="$ac_config_status_args --quiet" - exec 5>/dev/null - $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false - exec 5>>config.log - # Use ||, not &&, to avoid exiting from the if with $? = 1, which - # would make configure fail if this is the last instruction. - $ac_cs_success || { (exit 1); exit 1; } -fi - diff -Nru pbsim-1.0.3/configure.ac pbsim-1.0.3+git20180330.e014b1d+dfsg/configure.ac --- pbsim-1.0.3/configure.ac 2012-08-01 10:02:24.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/configure.ac 2018-03-30 08:36:07.000000000 +0000 @@ -2,10 +2,10 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ(2.61) -AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS) +AC_INIT([pbsim], [1.0.0], [pfaucon@asu.edu]) AC_CONFIG_SRCDIR([src/pbsim.cpp]) AC_CONFIG_HEADER([config.h]) -AM_INIT_AUTOMAKE(pbsim,1.0.0) +AM_INIT_AUTOMAKE # Checks for programs. AC_PROG_CXX diff -Nru pbsim-1.0.3/debian/changelog pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/changelog --- pbsim-1.0.3/debian/changelog 2017-01-31 10:31:06.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/changelog 2018-10-31 09:03:42.000000000 +0000 @@ -1,3 +1,16 @@ +pbsim (1.0.3+git20180330.e014b1d+dfsg-1) unstable; urgency=medium + + * Team upload. + * Add watch file using git mode + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.2.1 + * Secure URI in copyright format + * Homepage moved from googlecode to github + * Drop unneeded lintian-override + + -- Andreas Tille Wed, 31 Oct 2018 10:03:42 +0100 + pbsim (1.0.3-3) unstable; urgency=medium * Fix compiling with GCC 7. diff -Nru pbsim-1.0.3/debian/compat pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/compat --- pbsim-1.0.3/debian/compat 2016-03-17 23:17:25.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/compat 2018-10-31 09:03:42.000000000 +0000 @@ -1 +1 @@ -9 +11 diff -Nru pbsim-1.0.3/debian/control pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/control --- pbsim-1.0.3/debian/control 2017-01-31 10:30:59.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/control 2018-10-31 09:03:42.000000000 +0000 @@ -1,18 +1,19 @@ Source: pbsim -Section: science -Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss -Build-Depends: debhelper (>= 9), +Section: science +Priority: optional +Build-Depends: debhelper (>= 11~), asciidoctor -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbsim.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/pbsim.git -Homepage: https://code.google.com/archive/p/pbsim/ +Standards-Version: 4.2.1 +Vcs-Browser: https://salsa.debian.org/med-team/pbsim +Vcs-Git: https://salsa.debian.org/med-team/pbsim.git +Homepage: https://github.com/pfaucon/PBSIM-PacBio-Simulator Package: pbsim Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, + ${misc:Depends} Description: simulator for PacBio sequencing reads PacBio DNA sequencers produce two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of diff -Nru pbsim-1.0.3/debian/copyright pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/copyright --- pbsim-1.0.3/debian/copyright 2016-03-17 23:13:56.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/copyright 2018-10-31 09:03:42.000000000 +0000 @@ -1,6 +1,12 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: pbsim -Source: https://code.google.com/archive/p/pbsim/ +Source: https://github.com/pfaucon/PBSIM-PacBio-Simulator/ +Files-Excluded: */bin + */.gitignore + */*.cproj + */*.sln + depcomp + install-sh Files: * Copyright: © 2012 Michiaki Hamada (mhamada@k.u-tokyo.ac.jp) diff -Nru pbsim-1.0.3/debian/patches/0001-fix-for-gcc-7.patch pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/patches/0001-fix-for-gcc-7.patch --- pbsim-1.0.3/debian/patches/0001-fix-for-gcc-7.patch 2017-01-31 10:28:33.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/patches/0001-fix-for-gcc-7.patch 1970-01-01 00:00:00.000000000 +0000 @@ -1,21 +0,0 @@ -From: Sascha Steinbiss -Date: Tue, 31 Jan 2017 10:28:08 +0000 -Subject: fix for gcc-7 - ---- - src/pbsim.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/pbsim.cpp b/src/pbsim.cpp -index af1b7d8..77e3e5c 100644 ---- a/src/pbsim.cpp -+++ b/src/pbsim.cpp -@@ -371,7 +371,7 @@ int main (int argc, char** argv) { - - srand((unsigned int)seed); - -- if (argv[optind] == '\0') { -+ if (argv[optind] == NULL) { - print_help(); - exit(-1); - } diff -Nru pbsim-1.0.3/debian/patches/series pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/patches/series --- pbsim-1.0.3/debian/patches/series 2017-01-31 10:28:33.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -0001-fix-for-gcc-7.patch diff -Nru pbsim-1.0.3/debian/source/lintian-overrides pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/source/lintian-overrides --- pbsim-1.0.3/debian/source/lintian-overrides 2016-03-17 11:54:45.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/source/lintian-overrides 2018-10-31 09:03:42.000000000 +0000 @@ -1,5 +1,2 @@ -# Upstream has not moved to a new source repo -pbsim source: obsolete-url-in-packaging - # Upstream does not provide signed tarballs pbsim source: debian-watch-may-check-gpg-signature diff -Nru pbsim-1.0.3/debian/upstream/metadata pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/upstream/metadata --- pbsim-1.0.3/debian/upstream/metadata 2016-01-24 17:08:55.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/upstream/metadata 2018-10-31 09:03:42.000000000 +0000 @@ -1,12 +1,19 @@ Reference: - Author: Yukiteru Ono, Kiyoshi Asai and Michiaki Hamada - Title: "PBSIM: PacBio reads simulator - toward accurate genome assembly" - Journal: Bioinformatics - Year: 2013 - Volume: 29 - Number: 1 - Pages: 119-121 - DOI: 10.1093/bioinformatics/bts649 - PMID: 23129296 - URL: http://bioinformatics.oxfordjournals.org/content/29/1/119 - eprint: http://bioinformatics.oxfordjournals.org/content/29/1/119.full.pdf+html + Author: Yukiteru Ono and Kiyoshi Asai and Michiaki Hamada + Title: "PBSIM: PacBio reads simulator - toward accurate genome assembly" + Journal: Bioinformatics + Year: 2013 + Volume: 29 + Number: 1 + Pages: 119-121 + DOI: 10.1093/bioinformatics/bts649 + PMID: 23129296 + URL: http://bioinformatics.oxfordjournals.org/content/29/1/119 + eprint: http://bioinformatics.oxfordjournals.org/content/29/1/119.full.pdf+html +Registry: + - Name: OMICtools + Entry: OMICS_00253 + - Name: SciCrunch + Entry: SCR_002512 + - Name: bio.tools + Entry: PBSIM diff -Nru pbsim-1.0.3/debian/watch pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/watch --- pbsim-1.0.3/debian/watch 2016-03-17 23:10:04.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/debian/watch 2018-10-31 09:03:42.000000000 +0000 @@ -1 +1,7 @@ -# Upstream repo is no longer updated. +version=4 + +opts="mode=git,pretty=1.0.3+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \ + https://github.com/pfaucon/PBSIM-PacBio-Simulator.git HEAD + +# Asked for release tags +# https://github.com/pfaucon/PBSIM-PacBio-Simulator/issues/10 diff -Nru pbsim-1.0.3/depcomp pbsim-1.0.3+git20180330.e014b1d+dfsg/depcomp --- pbsim-1.0.3/depcomp 2012-08-01 10:02:26.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/depcomp 1970-01-01 00:00:00.000000000 +0000 @@ -1,589 +0,0 @@ -#! /bin/sh -# depcomp - compile a program generating dependencies as side-effects - -scriptversion=2007-03-29.01 - -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software -# Foundation, Inc. - -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2, or (at your option) -# any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. - -# As a special exception to the GNU General Public License, if you -# distribute this file as part of a program that contains a -# configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. - -# Originally written by Alexandre Oliva . - -case $1 in - '') - echo "$0: No command. 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This mechanism is used in libtool 1.4 series to - # handle both shared and static libraries in a single compilation. - # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d. - # - # With libtool 1.5 this exception was removed, and libtool now - # generates 2 separate objects for the 2 libraries. These two - # compilations output dependencies in $dir.libs/$base.o.d and - # in $dir$base.o.d. We have to check for both files, because - # one of the two compilations can be disabled. We should prefer - # $dir$base.o.d over $dir.libs/$base.o.d because the latter is - # automatically cleaned when .libs/ is deleted, while ignoring - # the former would cause a distcleancheck panic. - tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4 - tmpdepfile2=$dir$base.o.d # libtool 1.5 - tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5 - tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504 - "$@" -Wc,-MD - else - tmpdepfile1=$dir$base.o.d - tmpdepfile2=$dir$base.d - tmpdepfile3=$dir$base.d - tmpdepfile4=$dir$base.d - "$@" -MD - fi - - stat=$? - if test $stat -eq 0; then : - else - rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" - exit $stat - fi - - for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" - do - test -f "$tmpdepfile" && break - done - if test -f "$tmpdepfile"; then - sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" - # That's a tab and a space in the []. - sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" - else - echo "#dummy" > "$depfile" - fi - rm -f "$tmpdepfile" - ;; - -#nosideeffect) - # This comment above is used by automake to tell side-effect - # dependency tracking mechanisms from slower ones. - -dashmstdout) - # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o. - "$@" || exit $? - - # Remove the call to Libtool. - if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do - shift - done - shift - fi - - # Remove `-o $object'. - IFS=" " - for arg - do - case $arg in - -o) - shift - ;; - $object) - shift - ;; - *) - set fnord "$@" "$arg" - shift # fnord - shift # $arg - ;; - esac - done - - test -z "$dashmflag" && dashmflag=-M - # Require at least two characters before searching for `:' - # in the target name. This is to cope with DOS-style filenames: - # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. - "$@" $dashmflag | - sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" - rm -f "$depfile" - cat < "$tmpdepfile" > "$depfile" - tr ' ' ' -' < "$tmpdepfile" | \ -## Some versions of the HPUX 10.20 sed can't process this invocation -## correctly. Breaking it into two sed invocations is a workaround. - sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" - rm -f "$tmpdepfile" - ;; - -dashXmstdout) - # This case only exists to satisfy depend.m4. It is never actually - # run, as this mode is specially recognized in the preamble. - exit 1 - ;; - -makedepend) - "$@" || exit $? - # Remove any Libtool call - if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do - shift - done - shift - fi - # X makedepend - shift - cleared=no - for arg in "$@"; do - case $cleared in - no) - set ""; shift - cleared=yes ;; - esac - case "$arg" in - -D*|-I*) - set fnord "$@" "$arg"; shift ;; - # Strip any option that makedepend may not understand. Remove - # the object too, otherwise makedepend will parse it as a source file. - -*|$object) - ;; - *) - set fnord "$@" "$arg"; shift ;; - esac - done - obj_suffix="`echo $object | sed 's/^.*\././'`" - touch "$tmpdepfile" - ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" - rm -f "$depfile" - cat < "$tmpdepfile" > "$depfile" - sed '1,2d' "$tmpdepfile" | tr ' ' ' -' | \ -## Some versions of the HPUX 10.20 sed can't process this invocation -## correctly. Breaking it into two sed invocations is a workaround. - sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" - rm -f "$tmpdepfile" "$tmpdepfile".bak - ;; - -cpp) - # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout. - "$@" || exit $? - - # Remove the call to Libtool. - if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do - shift - done - shift - fi - - # Remove `-o $object'. - IFS=" " - for arg - do - case $arg in - -o) - shift - ;; - $object) - shift - ;; - *) - set fnord "$@" "$arg" - shift # fnord - shift # $arg - ;; - esac - done - - "$@" -E | - sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ - -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | - sed '$ s: \\$::' > "$tmpdepfile" - rm -f "$depfile" - echo "$object : \\" > "$depfile" - cat < "$tmpdepfile" >> "$depfile" - sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" - rm -f "$tmpdepfile" - ;; - -msvisualcpp) - # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o, - # because we must use -o when running libtool. - "$@" || exit $? - IFS=" " - for arg - do - case "$arg" in - "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") - set fnord "$@" - shift - shift - ;; - *) - set fnord "$@" "$arg" - shift - shift - ;; - esac - done - "$@" -E | - sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" - rm -f "$depfile" - echo "$object : \\" > "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" - echo " " >> "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" - rm -f "$tmpdepfile" - ;; - -none) - exec "$@" - ;; - -*) - echo "Unknown depmode $depmode" 1>&2 - exit 1 - ;; -esac - -exit 0 - -# Local Variables: -# mode: shell-script -# sh-indentation: 2 -# eval: (add-hook 'write-file-hooks 'time-stamp) -# time-stamp-start: "scriptversion=" -# time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" -# End: diff -Nru pbsim-1.0.3/.deps/pbsim.Po pbsim-1.0.3+git20180330.e014b1d+dfsg/.deps/pbsim.Po --- pbsim-1.0.3/.deps/pbsim.Po 2012-08-01 10:02:26.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/.deps/pbsim.Po 1970-01-01 00:00:00.000000000 +0000 @@ -1,154 +0,0 @@ -pbsim.o pbsim.o: pbsim.cpp config.h /usr/include/stdio.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h \ - /usr/lib/gcc/i386-redhat-linux/3.4.6/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/wordsize.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/i386-redhat-linux/3.4.6/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/endian.h /usr/include/bits/endian.h /usr/include/xlocale.h \ - /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h \ - /usr/include/alloca.h /usr/include/string.h /usr/include/ctype.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/i386-redhat-linux/3.4.6/include/limits.h \ - /usr/lib/gcc/i386-redhat-linux/3.4.6/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/sys/time.h /usr/include/sys/resource.h \ - /usr/include/bits/resource.h - -config.h: - -/usr/include/stdio.h: - -/usr/include/features.h: - -/usr/include/sys/cdefs.h: - -/usr/include/gnu/stubs.h: - -/usr/lib/gcc/i386-redhat-linux/3.4.6/include/stddef.h: - -/usr/include/bits/types.h: - -/usr/include/bits/wordsize.h: - -/usr/include/bits/typesizes.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/i386-redhat-linux/3.4.6/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/xlocale.h: - -/usr/include/sys/types.h: - -/usr/include/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/bits/time.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/sched.h: - -/usr/include/alloca.h: - -/usr/include/string.h: - -/usr/include/ctype.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -/usr/lib/gcc/i386-redhat-linux/3.4.6/include/limits.h: - -/usr/lib/gcc/i386-redhat-linux/3.4.6/include/syslimits.h: - -/usr/include/limits.h: - -/usr/include/bits/posix1_lim.h: - -/usr/include/bits/local_lim.h: - -/usr/include/linux/limits.h: - -/usr/include/bits/posix2_lim.h: - -/usr/include/bits/xopen_lim.h: - -/usr/include/sys/time.h: - -/usr/include/sys/resource.h: - -/usr/include/bits/resource.h: diff -Nru pbsim-1.0.3/INSTALL pbsim-1.0.3+git20180330.e014b1d+dfsg/INSTALL --- pbsim-1.0.3/INSTALL 2012-08-01 10:02:24.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/INSTALL 2018-03-30 08:36:07.000000000 +0000 @@ -38,9 +38,10 @@ may remove or edit it. The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You need `configure.ac' if -you want to change it or regenerate `configure' using a newer version -of `autoconf'. +`configure' by a perl program called `autoreconf' (see autoreconf -h +for details). `Makefile.in` is also generated from `Makefile.am`. +You need `configure.ac' if you want to change it or regenerate +`configure' using a newer version of `autoreconf'. The simplest way to compile this package is: diff -Nru pbsim-1.0.3/install-sh pbsim-1.0.3+git20180330.e014b1d+dfsg/install-sh --- pbsim-1.0.3/install-sh 2012-08-01 10:02:25.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/install-sh 1970-01-01 00:00:00.000000000 +0000 @@ -1,519 +0,0 @@ -#!/bin/sh -# install - install a program, script, or datafile - -scriptversion=2006-12-25.00 - -# This originates from X11R5 (mit/util/scripts/install.sh), which was -# later released in X11R6 (xc/config/util/install.sh) with the -# following copyright and license. -# -# Copyright (C) 1994 X Consortium -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to -# deal in the Software without restriction, including without limitation the -# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or -# sell copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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You may need the \`Bison' package - in order for those modifications to take effect. You can get - \`Bison' from any GNU archive site." - rm -f y.tab.c y.tab.h - if test $# -ne 1; then - eval LASTARG="\${$#}" - case $LASTARG in - *.y) - SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'` - if test -f "$SRCFILE"; then - cp "$SRCFILE" y.tab.c - fi - SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'` - if test -f "$SRCFILE"; then - cp "$SRCFILE" y.tab.h - fi - ;; - esac - fi - if test ! -f y.tab.h; then - echo >y.tab.h - fi - if test ! -f y.tab.c; then - echo 'main() { return 0; }' >y.tab.c - fi - ;; - - lex|flex) - echo 1>&2 "\ -WARNING: \`$1' is $msg. You should only need it if - you modified a \`.l' file. You may need the \`Flex' package - in order for those modifications to take effect. 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You should only need it if - you modified a \`.texi' or \`.texinfo' file, or any other file - indirectly affecting the aspect of the manual. The spurious - call might also be the consequence of using a buggy \`make' (AIX, - DU, IRIX). You might want to install the \`Texinfo' package or - the \`GNU make' package. Grab either from any GNU archive site." - # The file to touch is that specified with -o ... - file=`echo "$*" | sed -n "$sed_output"` - test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` - if test -z "$file"; then - # ... or it is the one specified with @setfilename ... - infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` - file=`sed -n ' - /^@setfilename/{ - s/.* \([^ ]*\) *$/\1/ - p - q - }' $infile` - # ... or it is derived from the source name (dir/f.texi becomes f.info) - test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info - fi - # If the file does not exist, the user really needs makeinfo; - # let's fail without touching anything. - test -f $file || exit 1 - touch $file - ;; - - tar) - shift - - # We have already tried tar in the generic part. - # Look for gnutar/gtar before invocation to avoid ugly error - # messages. - if (gnutar --version > /dev/null 2>&1); then - gnutar "$@" && exit 0 - fi - if (gtar --version > /dev/null 2>&1); then - gtar "$@" && exit 0 - fi - firstarg="$1" - if shift; then - case $firstarg in - *o*) - firstarg=`echo "$firstarg" | sed s/o//` - tar "$firstarg" "$@" && exit 0 - ;; - esac - case $firstarg in - *h*) - firstarg=`echo "$firstarg" | sed s/h//` - tar "$firstarg" "$@" && exit 0 - ;; - esac - fi - - echo 1>&2 "\ -WARNING: I can't seem to be able to run \`tar' with the given arguments. - You may want to install GNU tar or Free paxutils, or check the - command line arguments." - exit 1 - ;; - - *) - echo 1>&2 "\ -WARNING: \`$1' is needed, and is $msg. - You might have modified some files without having the - proper tools for further handling them. Check the \`README' file, - it often tells you about the needed prerequisites for installing - this package. You may also peek at any GNU archive site, in case - some other package would contain this missing \`$1' program." - exit 1 - ;; -esac - -exit 0 - -# Local variables: -# eval: (add-hook 'write-file-hooks 'time-stamp) -# time-stamp-start: "scriptversion=" -# time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" -# End: diff -Nru pbsim-1.0.3/README pbsim-1.0.3+git20180330.e014b1d+dfsg/README --- pbsim-1.0.3/README 2012-10-04 07:51:19.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/README 2018-03-30 08:36:07.000000000 +0000 @@ -1,4 +1,10 @@ -1. About PBSIM +This Repository +================== + +This repository was created because the [Google Code repository](https://code.google.com/archive/p/pbsim/downloads) provided by the original authors is not being maintained, and Google Code is now defunct. + + +About PBSIM ============== PacBio sequencers produce two types of characteristic reads as below. @@ -10,7 +16,21 @@ sampling-based and model-based simulations are implemented. -2. Run PBSIM with sample data +Building PBSIM +================ + +To build PBSIM run; + +```bash + + autoreconf -i + ./configure + make + ``` + +A new executable pbsim will be available in the src/ directory + +Run PBSIM with sample data ============================= To run model-based simulation: @@ -73,7 +93,7 @@ sample/sample.fasta -3. Model-based simulation +Model-based simulation ========================= For each read, the length is randomly drawn from the log-normal distribution @@ -118,7 +138,7 @@ of CLR reads. -4. Sampling-based simulation +Sampling-based simulation ============================ The lengths and quality scores of reads are simulated by randomly @@ -129,7 +149,7 @@ the same as model-based simulation. -5. Input files +Input files ============== PBSIM requires reference sequences in the single- or multi-FASTA Format. @@ -139,7 +159,7 @@ FASTQ format must be Sanger standard (fastq-sanger). -6. Output files +Output files =============== If a reference sequence file is multi-FASTA format, simulated datasets @@ -155,7 +175,7 @@ "sd" is prefix which can be specified with the --prefix option. -7. Quality profile +Quality profile ================== Quality profiles are derived from frequencies of real quality scores @@ -167,7 +187,7 @@ columns are proportions of phred quality scores (0-93). -8. Runtime and memory +Runtime and memory ===================== When a coverage depth is 100x and a length of reference sequence is about 10M, @@ -178,3 +198,9 @@ PBSIM requires memory of the length of reference sequence plus several mega bytes. + +Contributors +===================== +@kiwiroy - autotools and warning corrections + +@jumpinsky - fixed memory leaks diff -Nru pbsim-1.0.3/README.md pbsim-1.0.3+git20180330.e014b1d+dfsg/README.md --- pbsim-1.0.3/README.md 1970-01-01 00:00:00.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/README.md 2018-03-30 08:36:07.000000000 +0000 @@ -0,0 +1,206 @@ +This Repository +================== + +This repository was created because the [Google Code repository](https://code.google.com/archive/p/pbsim/downloads) provided by the original authors is not being maintained, and Google Code is now defunct. + + +About PBSIM +============== + +PacBio sequencers produce two types of characteristic reads as below. + + Continuous Long Read (CLR) : long and high error rate. + Circular consensus Read (CCS) : short and low error rate. + +We have developed a PacBio reads simulater (called PBSIM) in which +sampling-based and model-based simulations are implemented. + + +Building PBSIM +================ + +To build PBSIM run; + +```bash + + autoreconf -i + ./configure + make + ``` + +A new executable pbsim will be available in the src/ directory + +Run PBSIM with sample data +============================= + +To run model-based simulation: + + pbsim --data-type CLR + --depth 20 + --model_qc data/model_qc_clr + sample/sample.fasta + +In the example above, simulated read sequences are randomly sampled from +a reference sequence ("sample/sample.fasta") and differences (errors) of +the sampled reads are introduced. +Data type is CLR, and coverage depth is 20. +If the reference sequence is multi-FASTA file, the simulated data is created +for each FASTA. Three output files are created for each FASTA. +"sd_0001.ref" is a single-FASTA file which is copied from the reference +sequence. +"sd_0001.fastq" is a simulated read dataset in the FASTQ format. +"sd_0001.maf" is a list of alignments between reference sequence and +simulated reads in the MAF format. +The length and accuracy of reads are simulated based on our model of PacBio +read. + +To run sampling-based simulation: + + pbsim --data-type CLR + --depth 20 + --sample-fastq sample/sample.fastq + sample/sample.fasta + +In the sampling-based simulation, read length and quality score are +the same as those of a read taken randomly in the sample PacBio dataset +("sample/sample.fastq"). + +If you want to create several simulated data with different coverage depths +using the same PacBio sample, you would be better to use --sample-profile-id +option as below. You can save time to parse "sample/sample.fastq". + + (1) storing profile + + pbsim --data-type CLR + --depth 20 + --prefix depth20 + --sample-fastq sample/sample.fastq + --sample-profile-id pf1 + sample/sample.fasta + + (2) reusing profile + + pbsim --data-type CLR + --depth 30 + --prefix depth30 + --sample-profile-id pf1 + sample/sample.fasta + + pbsim --data-type CLR + --depth 40 + --prefix depth40 + --sample-profile-id pf1 + sample/sample.fasta + + +Model-based simulation +========================= + +For each read, the length is randomly drawn from the log-normal distribution +with given mean and standard deviation. + +How to simulate the accuracy of each read is different between CLR and CCS +read. For CLR reads, the accuracy is randomly drawn from the normal +distribution with given mean and standard deviation. For CCS reads, +an exponential function which is fit to the the real distribution is +utilized to simulate with fixed mean and standard deviation. + +Errors from single molecule sequencing which generates PacBio reads are +considered to be stochastical, therefore quality scores are randomly chosen +from a frequency table of quality scores (named "quality profile") for each +accuracy of a read. For accuracies of 0-59% and 86-100% of CLR readsi and +0-84% of CCS reads, uniform distributions are used because real PacBio +datasets are not sufficiently large. +"data/model_qc_clr" is quality profile for CLR and +"data/model_qc_ccs" is for CCS. + +Simulated read sequences are randomly sampled from a reference sequence. +The percentage of both directions of reads is same. Differences (errors) +of the sampled reads are introduced as follows. +The substitutions and insertions are introduced according to the quality +scores. Their probabilities are computed for each positions of a simulated +read from the error probability of the position (computed from the quality +score of the position) and the ratios of differences given by the user. +Patterns of substitutions are randomly sampled. +We observed that inserted nucleotides are often the same as their following +nucleotides. According to the observed bias, half of inserted nucleotides +are chosen to be the same as their following nucleotides, and the other +half are randomly chosen. +The deletion probability is uniform for all positions of all simulated +reads, which is computed from the mean error probability of the read set +and the ratios of differeces. + +By setting minimum and maximum of the length, the range of length chosen +from the distribution model can be restricted. Note that mean and standard +deviation of the chosen length are influenced by this restriction. +The accuracy can be restricted in the same way, however unlike the length, +the restriction of accuracy is not strict, and can be used in only case +of CLR reads. + + +Sampling-based simulation +============================ + +The lengths and quality scores of reads are simulated by randomly +sampling them in a real library of PacBio reads provided by the user. +randomly in a real PacBio dataset given by user. Subsequently, their +nucleotide sequences are simulated by the same method with the model- +based simulation. The restriction of length and accuracy are also +the same as model-based simulation. + + +Input files +============== + +PBSIM requires reference sequences in the single- or multi-FASTA Format. + +A real PacBio read data is required for sampling-based simulation, +specified with the --sample-fastq option. +FASTQ format must be Sanger standard (fastq-sanger). + + +Output files +=============== + +If a reference sequence file is multi-FASTA format, simulated datasets +are generated for each reference sequence numbered sequentially. +Three output files are created for each reference sequence. + +"sd_.ref" is a single-FASTA file which is copied from the reference +sequence. +"sd_.fastq" is a simulated read dataset in the FASTQ format. +"sd_.maf" is a list of alignments between reference sequence and +simulated reads in the MAF format. + +"sd" is prefix which can be specified with the --prefix option. + + +Quality profile +================== + +Quality profiles are derived from frequencies of real quality scores +for each accuracy of a read. +"data/model_qc_clr" is quality profile for CLR, "data/model_qc_ccs" is for CCS. +In "data/model_qc_clr", 1st column is accuracies of a read, and 2nd-23th +columns are proportions of phred quality scores (0-21). +In "data/model_qc_ccs", 1st column is accuracies of a read, and 2nd-95th +columns are proportions of phred quality scores (0-93). + + +Runtime and memory +===================== + +When a coverage depth is 100x and a length of reference sequence is about 10M, +PBSIM generates simulated dataset in several minutes. +The runtime is roughly proportional to the coverage depth and the length of +reference sequence. + +PBSIM requires memory of the length of reference sequence plus several mega +bytes. + + +Contributors +===================== +@kiwiroy - autotools and warning corrections + +@jumpinsky - fixed memory leaks diff -Nru pbsim-1.0.3/src/defines.h pbsim-1.0.3+git20180330.e014b1d+dfsg/src/defines.h --- pbsim-1.0.3/src/defines.h 1970-01-01 00:00:00.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/src/defines.h 2018-03-30 08:36:07.000000000 +0000 @@ -0,0 +1,22 @@ +#pragma once + +#define SUCCEEDED 1 +#define FAILED 0 +#define TRUE 1 +#define FALSE 0 +#define BUF_SIZE 10240 +#define REF_ID_LEN_MAX 128 +#define REF_SEQ_NUM_MAX 9999 +#define REF_SEQ_LEN_MAX 1000000000 +#define REF_SEQ_LEN_MIN 100 +#define FASTQ_NUM_MAX 100000000 +#define FASTQ_LEN_MAX 1000000 +#define EXISTS_LINE_FEED 1 +#define DEPTH_MAX 1000 +#define RATIO_MAX 1000 +#define DATA_TYPE_CLR 0 +#define DATA_TYPE_CCS 1 +#define PROCESS_MODEL 1 +#define PROCESS_SAMPLING 2 +#define PROCESS_SAMPLING_REUSE 3 +#define PROCESS_SAMPLING_STORE 4 diff -Nru pbsim-1.0.3/src/.deps/pbsim.Po pbsim-1.0.3+git20180330.e014b1d+dfsg/src/.deps/pbsim.Po --- pbsim-1.0.3/src/.deps/pbsim.Po 2012-09-14 03:41:20.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/src/.deps/pbsim.Po 1970-01-01 00:00:00.000000000 +0000 @@ -1,153 +0,0 @@ -pbsim.o pbsim.o: pbsim.cpp ../config.h /usr/include/stdio.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/endian.h /usr/include/bits/endian.h /usr/include/xlocale.h \ - /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/include/string.h /usr/include/ctype.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/sys/time.h /usr/include/sys/resource.h \ - /usr/include/bits/resource.h - -../config.h: - -/usr/include/stdio.h: - -/usr/include/features.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/xlocale.h: - -/usr/include/sys/types.h: - -/usr/include/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/bits/time.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/alloca.h: - -/usr/include/string.h: - -/usr/include/ctype.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: - -/usr/include/limits.h: - -/usr/include/bits/posix1_lim.h: - -/usr/include/bits/local_lim.h: - -/usr/include/linux/limits.h: - -/usr/include/bits/posix2_lim.h: - -/usr/include/bits/xopen_lim.h: - -/usr/include/sys/time.h: - -/usr/include/sys/resource.h: - -/usr/include/bits/resource.h: diff -Nru pbsim-1.0.3/src/helpers.cpp pbsim-1.0.3+git20180330.e014b1d+dfsg/src/helpers.cpp --- pbsim-1.0.3/src/helpers.cpp 1970-01-01 00:00:00.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/src/helpers.cpp 2018-03-30 08:36:07.000000000 +0000 @@ -0,0 +1,84 @@ +#include +#include +#include + +/////////////////////////////////////// +// Function: trim - Remove "\n" // +/////////////////////////////////////// + +int trim(char *line) { + int end_pos = strlen(line) - 1; + + if (line[end_pos] == '\n') { + line[end_pos] = '\0'; + return 1; + } + return 0; +} + +/////////////////////////////////////////////////////// +// Function: get_time_cpu - Get CPU time // +/////////////////////////////////////////////////////// + +long get_time_cpu() { + struct rusage ru; + getrusage(RUSAGE_SELF, &ru); + return ru.ru_utime.tv_sec; +} + +/////////////////////////////////////////////////////// +// Function: get_time - Get time // +/////////////////////////////////////////////////////// + +long get_time() { + struct timeval tv; + gettimeofday(&tv, NULL); + return tv.tv_sec; +} + +///////////////////////////////////////// +// Function: count_digit - count digit // +///////////////////////////////////////// + +int count_digit(long num) { + int digit = 1; + int quotient; + + quotient = int(num / 10); + + while (quotient != 0) { + digit ++; + quotient = int(quotient / 10); + } + + return digit; +} + +////////////////////////////////////////////////////// +// Function: revcomp - convert to reverse complement// +////////////////////////////////////////////////////// + +void revcomp(char* str) { + int i, len; + char c; + + len = strlen(str); + + for(i=0; i + +#include "defines.h" +#include "structures.h" + +///////////////////////////////////////////////////////////// +// Function: print_sim_param - Print simulation parameters // +///////////////////////////////////////////////////////////// + +void print_sim_param(const sim_t *sim) { + fprintf(stderr, ":::: Simulation parameters :::\n\n"); + + if (sim->process == PROCESS_MODEL) { + fprintf(stderr, "Simulated by stochastic model.\n\n"); + } else { + fprintf(stderr, "Simulated by fastq sampling.\n\n"); + } + + fprintf(stderr, "prefix : %s\n", sim->prefix); + if (sim->set_flg[14]) { + fprintf(stderr, "sample_profile_id : %s\n", sim->profile_id); + } + + if (sim->data_type == DATA_TYPE_CLR) { + fprintf(stderr, "data-type : CLR\n"); + } else { + fprintf(stderr, "data-type : CCS\n"); + } + + fprintf(stderr, "depth : %lf\n", sim->depth); + + if (sim->set_flg[0]) { + fprintf(stderr, "length-mean : (sampling FASTQ)\n"); + fprintf(stderr, "length-sd : (sampling FASTQ)\n"); + } else { + fprintf(stderr, "length-mean : %f\n", sim->len_mean); + fprintf(stderr, "length-sd : %f\n", sim->len_sd); + } + fprintf(stderr, "length-min : %ld\n", sim->len_min); + fprintf(stderr, "length-max : %ld\n", sim->len_max); + + if (sim->set_flg[0]) { + fprintf(stderr, "accuracy-mean : (sampling FASTQ)\n"); + fprintf(stderr, "accuracy-sd : (sampling FASTQ)\n"); + } else { + fprintf(stderr, "accuracy-mean : %f\n", sim->accuracy_mean); + fprintf(stderr, "accuracy-sd : %f\n", sim->accuracy_sd); + } + fprintf(stderr, "accuracy-min : %f\n", sim->accuracy_min); + fprintf(stderr, "accuracy-max : %f\n", sim->accuracy_max); + + fprintf(stderr, "difference-ratio : %ld:%ld:%ld\n", + sim->sub_ratio, sim->ins_ratio, sim->del_ratio); + + fprintf(stderr, "\n"); +} + +///////////////////////////////////////////////////// +// Function: print_fastq_stats - Print FASTQ stats // +///////////////////////////////////////////////////// + +void print_fastq_stats(const sim_t *sim, const fastq_t *fastq) { + fprintf(stderr, ":::: FASTQ stats ::::\n\n"); + + if (sim->process == PROCESS_SAMPLING_REUSE) { + fprintf(stderr, "file name : %s\n", sim->profile_fq); + } else { + fprintf(stderr, "file name : %s\n", fastq->file); + fprintf(stderr, "\n:: all reads ::\n"); + fprintf(stderr, "read num. : %ld\n", fastq->num); + fprintf(stderr, "read total length : %lld\n", fastq->len_total); + fprintf(stderr, "read min length : %ld\n", fastq->len_min); + fprintf(stderr, "read max length : %ld\n", fastq->len_max); + } + + fprintf(stderr, "\n:: filtered reads ::\n"); + fprintf(stderr, "read num. : %ld\n", fastq->num_filtered); + fprintf(stderr, "read total length : %lld\n", fastq->len_total_filtered); + fprintf(stderr, "read min length : %ld\n", fastq->len_min_filtered); + fprintf(stderr, "read max length : %ld\n", fastq->len_max_filtered); + fprintf(stderr, "read length mean (SD) : %f (%f)\n", + fastq->len_mean_filtered, fastq->len_sd_filtered); + fprintf(stderr, "read accuracy mean (SD) : %f (%f)\n", + fastq->accuracy_mean_filtered, fastq->accuracy_sd_filtered); + fprintf(stderr, "\n"); +} + +//////////////////////////////////////////////////////////////// +// Function: print_simulation_stats - Print Simulation Stats. // +//////////////////////////////////////////////////////////////// + +void print_simulation_stats(const sim_t *sim, const ref_t *ref) { + double res_depth = (double)sim->res_len_total / ref->len; + double res_sub_rate = (double)sim->res_sub_num / sim->res_len_total; + double res_ins_rate = (double)sim->res_ins_num / sim->res_len_total; + double res_del_rate = (double)sim->res_del_num / sim->res_len_total; + + fprintf(stderr, ":::: Simulation stats (ref.%ld - name: %s) ::::\n\n", ref->num, ref->id); + fprintf(stderr, "read num. : %ld\n", sim->res_num); + fprintf(stderr, "depth : %lf\n", res_depth); + fprintf(stderr, "read length mean (SD) : %f (%f)\n", + sim->res_len_mean, sim->res_len_sd); + fprintf(stderr, "read length min : %ld\n", sim->res_len_min); + fprintf(stderr, "read length max : %ld\n", sim->res_len_max); + fprintf(stderr, "read accuracy mean (SD) : %f (%f)\n", + sim->res_accuracy_mean, sim->res_accuracy_sd); + fprintf(stderr, "substitution rate. : %f\n", res_sub_rate); + fprintf(stderr, "insertion rate. : %f\n", res_ins_rate); + fprintf(stderr, "deletion rate. : %f\n", res_del_rate); + fprintf(stderr, "\n"); +} + +/////////////////////////////////////// +// Function: print_help - Print help // +/////////////////////////////////////// + +void print_help() { + fprintf(stderr, "\n"); + fprintf(stderr, "USAGE: pbsim [options] \n\n"); + fprintf(stderr, " FASTA format file.\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " [general options]\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " --prefix prefix of output files (sd).\n"); + fprintf(stderr, " --data-type data type. CLR or CCS (CLR).\n"); + fprintf(stderr, " --depth depth of coverage (CLR: 20.0, CCS: 50.0).\n"); + fprintf(stderr, " --length-min minimum length (100).\n"); + fprintf(stderr, " --length-max maximum length (CLR: 25000, CCS: 2500).\n"); + fprintf(stderr, " --accuracy-min minimum accuracy.\n"); + fprintf(stderr, " (CLR: 0.75, CCS: fixed as 0.75).\n"); + fprintf(stderr, " this option can be used only in case of CLR.\n"); + fprintf(stderr, " --accuracy-max maximum accuracy.\n"); + fprintf(stderr, " (CLR: 1.00, CCS: fixed as 1.00).\n"); + fprintf(stderr, " this option can be used only in case of CLR.\n"); + fprintf(stderr, " --difference-ratio ratio of differences. substitution:insertion:deletion.\n"); + fprintf(stderr, " each value up to 1000 (CLR: 10:60:30, CCS:6:21:73).\n"); + fprintf(stderr, " --seed for a pseudorandom number generator (Unix time).\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " [options of sampling-based simulation]\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " --sample-fastq FASTQ format file to sample.\n"); + fprintf(stderr, " --sample-profile-id sample-fastq (filtered) profile ID.\n"); + fprintf(stderr, " when using --sample-fastq, profile is stored.\n"); + fprintf(stderr, " 'sample_profile_.fastq', and\n"); + fprintf(stderr, " 'sample_profile_.stats' are created.\n"); + fprintf(stderr, " when not using --sample-fastq, profile is re-used.\n"); + fprintf(stderr, " Note that when profile is used, --length-min,max,\n"); + fprintf(stderr, " --accuracy-min,max would be the same as the profile.\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " [options of model-based simulation].\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " --model_qc model of quality code.\n"); + fprintf(stderr, " --length-mean mean of length model (CLR: 3000.0, CCS:450.0).\n"); + fprintf(stderr, " --length-sd standard deviation of length model.\n"); + fprintf(stderr, " (CLR: 2300.0, CCS: 170.0).\n"); + fprintf(stderr, " --accuracy-mean mean of accuracy model.\n"); + fprintf(stderr, " (CLR: 0.78, CCS: fixed as 0.98).\n"); + fprintf(stderr, " this option can be used only in case of CLR.\n"); + fprintf(stderr, " --accuracy-sd standard deviation of accuracy model.\n"); + fprintf(stderr, " (CLR: 0.02, CCS: fixed as 0.02).\n"); + fprintf(stderr, " this option can be used only in case of CLR.\n"); + fprintf(stderr, "\n"); +} \ No newline at end of file diff -Nru pbsim-1.0.3/src/output.h pbsim-1.0.3+git20180330.e014b1d+dfsg/src/output.h --- pbsim-1.0.3/src/output.h 1970-01-01 00:00:00.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/src/output.h 2018-03-30 08:36:07.000000000 +0000 @@ -0,0 +1,6 @@ +#pragma once + +void print_sim_param(const sim_t *sim); +void print_fastq_stats(const sim_t *sim, const fastq_t *fastq); +void print_simulation_stats(const sim_t *sim, const ref_t *ref); +void print_help(); diff -Nru pbsim-1.0.3/src/pbsim.cpp pbsim-1.0.3+git20180330.e014b1d+dfsg/src/pbsim.cpp --- pbsim-1.0.3/src/pbsim.cpp 2013-09-01 12:52:53.000000000 +0000 +++ pbsim-1.0.3+git20180330.e014b1d+dfsg/src/pbsim.cpp 2018-03-30 08:36:07.000000000 +0000 @@ -10,162 +10,218 @@ #include #include #include -#include -#include +#include // min -#define SUCCEEDED 1 -#define FAILED 0 -#define TRUE 1 -#define FALSE 0 -#define BUF_SIZE 10240 -#define REF_ID_LEN_MAX 128 -#define REF_SEQ_NUM_MAX 9999 -#define REF_SEQ_LEN_MAX 1000000000 -#define REF_SEQ_LEN_MIN 100 -#define FASTQ_NUM_MAX 100000000 -#define FASTQ_LEN_MAX 1000000 -#define EXISTS_LINE_FEED 1 -#define DEPTH_MAX 1000 -#define RATIO_MAX 1000 -#define DATA_TYPE_CLR 0 -#define DATA_TYPE_CCS 1 -#define PROCESS_MODEL 1 -#define PROCESS_SAMPLING 2 -#define PROCESS_SAMPLING_REUSE 3 -#define PROCESS_SAMPLING_STORE 4 - -///////////////////////////////////////// -// Definitions of structures // -///////////////////////////////////////// - -// simulation parameters -struct sim_t { - int data_type; - int process; - double depth; - double accuracy_mean, accuracy_sd, accuracy_max, accuracy_min; - long len_min, len_max; - double len_mean, len_sd; - long long len_quota; - long sub_ratio, ins_ratio, del_ratio; - double sub_rate, ins_rate, del_rate; - int set_flg[20]; - long res_num; - long long res_len_total; - double res_depth; - double res_accuracy_mean, res_accuracy_sd; - long res_len_min, res_len_max; - double res_len_mean, res_len_sd; - long res_sub_num, res_ins_num, res_del_num; - double res_sub_rate, res_ins_rate, res_del_rate; - char *prefix, *outfile_ref, *outfile_fq, *outfile_maf; - char *model_qc_file; - char *profile_id, *profile_fq, *profile_stats; -}; - -// FASTQ -struct fastq_t { - char *file; - long num; - long long len_total; - long len_min, len_max; - long num_filtered; - long long len_total_filtered; - long len_min_filtered, len_max_filtered; - double len_mean_filtered, len_sd_filtered; - double accuracy_mean_filtered, accuracy_sd_filtered; -}; - -// Reference -struct ref_t { - char *file; - char *seq; - char id[REF_ID_LEN_MAX + 1]; - long len; - long num_seq; - long num; -}; - -// Mutation -struct mut_t { - long sub_thre[94], ins_thre[94], del_thre; - char *sub_nt_a, *sub_nt_t, *sub_nt_g, *sub_nt_c, *sub_nt_n, *ins_nt; - char *qc, *new_qc, *tmp_qc, *seq, *new_seq, *maf_seq, *maf_ref_seq; - long tmp_len_max; - char seq_strand; - long seq_left, seq_right; -}; - -// Quality code -struct qc_t { - char character; - double prob; -}; - -// Quality code of model -struct model_qc_t { - int min; - int max; - double prob[94]; -}; +#include "defines.h" +#include "structures.h" +#include "output.h" // printing code is here +#include "helpers.h" // string manipulation and time ///////////////////////////////////////// // Global variances // ///////////////////////////////////////// FILE *fp_filtered, *fp_stats, *fp_ref, *fp_fq, *fp_maf; -struct sim_t sim; struct fastq_t fastq; -struct ref_t ref; struct mut_t mut; -struct qc_t qc[94]; struct model_qc_t model_qc[101]; long freq_len[FASTQ_LEN_MAX + 1]; long freq_accuracy[100000 + 1]; +const char *versionString = "1.0.4"; + ///////////////////////////////////////// // Prototypes of functions // ///////////////////////////////////////// -int trim(char *line); -void init_sim_res(); -int set_sim_param(); -int get_ref_inf(); -int get_ref_seq(); -int get_fastq_inf(); -int set_model_qc(); -int set_mut(); -int simulate_by_sampling(); -int simulate_by_model(); -int mutate(); -int count_digit(long num); -void print_sim_param(); -void print_fastq_stats(); -void print_simulation_stats(); -void print_help(); -void revcomp(char* str); -long get_time_cpu(); -long get_time(); +void parse_options(int argc, char** argv, sim_t *sim); +void init_sim_res(sim_t *sim); +int initialize_sim_process(sim_t *sim, fastq_t *fastq, qc_t *qc); +int set_sim_param(sim_t *sim); +int get_ref_inf(const sim_t *sim, ref_t *ref); +int get_ref_seq(const sim_t *sim, ref_t *ref); +int get_fastq_inf(const sim_t *sim, const qc_t *qc); +int set_model_qc(const sim_t *sim); +int set_mut(sim_t *sim); +int simulate_by_sampling(sim_t *sim, ref_t *ref, mut_t *mut, fastq_t *fastq, qc_t *qc); +int simulate_by_model(sim_t *sim, ref_t *ref, qc_t *qc); +int mutate(sim_t *sim, ref_t *ref); ///////////////////////////////////////// // Main // ///////////////////////////////////////// int main (int argc, char** argv) { - char *tp, *tmp_buf; long len; - long num; - long ratio; long i, j; long rst1, rst2; long t1, t2; + struct sim_t sim; + struct qc_t qc[94]; + struct ref_t ref; rst1 = get_time_cpu(); t1 = get_time(); - memset(sim.set_flg, 0, sizeof(sim.set_flg)); + ////// Check Input + parse_options(argc, argv, &sim); + + if (argv[optind] == NULL) { + print_help(); + exit(-1); + } + + ///// Initialize + + // Quality code to error probability + for (i=0; i<=93; i++) { + qc[i].prob = pow(10, (double)i / -10); + qc[i].character = (char)(i+33); + } + + if(initialize_sim_process(&sim, &fastq, qc) == FAILED) + exit(-1); + + // Reference sequence + if ((ref.file = (char *)malloc(strlen(argv[optind]) + 1)) == 0) { + fprintf(stderr, "ERROR: Cannot allocate memory.\n"); + exit(-1); + } + strcpy(ref.file, argv[optind]); + fprintf(stderr, "!! ref file %s\n", ref.file); + + if (get_ref_inf(&sim, &ref) == FAILED) { + exit(-1); + } + + // Set mutation parameters and varianeces + if (set_mut(&sim) == FAILED) { + exit(-1); + } + + // Creating simulated reads + for (ref.num=1; ref.num<=ref.num_seq; ref.num++) { + if (get_ref_seq(&sim, &ref) == FAILED) { + exit(-1); + } + + init_sim_res(&sim); + + sprintf(sim.outfile_fq, "%s_%04ld.fastq", sim.prefix, ref.num); + if ((fp_fq = fopen(sim.outfile_fq, "w")) == NULL) { + fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim.outfile_fq); + return FAILED; + } + + sprintf(sim.outfile_maf, "%s_%04ld.maf", sim.prefix, ref.num); + if ((fp_maf = fopen(sim.outfile_maf, "w")) == NULL) { + fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim.outfile_maf); + fclose(fp_fq); + return FAILED; + } + + sim.len_quota = (long long)(sim.depth * ref.len); + + if (sim.process == PROCESS_MODEL) { + if (simulate_by_model(&sim, &ref, qc) == FAILED) { + exit(-1); + } + } else { + if (simulate_by_sampling(&sim, &ref, &mut, &fastq, qc) == FAILED) { + exit(-1); + } + } + + print_simulation_stats(&sim, &ref); + + fclose(fp_fq); + fclose(fp_maf); + } + + if ((sim.process == PROCESS_SAMPLING_STORE) || (sim.process == PROCESS_SAMPLING_REUSE)) { + fclose(fp_filtered); + fclose(fp_stats); + } + + rst2 = get_time_cpu(); + t2 = get_time(); + + fprintf(stderr, ":::: System utilization ::::\n\n"); + fprintf(stderr, "CPU time(s) : %ld\n", rst2 - rst1); + fprintf(stderr, "Elapsed time(s) : %ld\n", t2 - t1); + + return(0); +} + +/////////////////////////////////////////////////////////////// +// Function: initialize_sim_process - perform the sim process requested // +/////////////////////////////////////////////////////////////// + +int initialize_sim_process(sim_t *sim, fastq_t *fastq, qc_t *qc) +{ +// Setting of simulation parameters + if (set_sim_param(sim) == FAILED) { + exit(-1); + } + print_sim_param(sim); + + switch(sim->process){ + case PROCESS_SAMPLING: + if ((fp_filtered = tmpfile()) == NULL) { + fprintf(stderr, "ERROR: Cannot open temporary file\n"); + return FAILED; + } + break; + case PROCESS_SAMPLING_STORE: + if ((fp_filtered = fopen(sim->profile_fq, "w+")) == NULL) { + fprintf(stderr, "ERROR: Cannot open filtered sample_profile\n"); + return FAILED; + } + if ((fp_stats = fopen(sim->profile_stats, "w+")) == NULL) { + fprintf(stderr, "ERROR: Cannot open stats sample_profile\n"); + return FAILED; + } + break; + case PROCESS_SAMPLING_REUSE: + if ((fp_filtered = fopen(sim->profile_fq, "r")) == NULL) { + fprintf(stderr, "ERROR: Cannot open sample_profile\n"); + return FAILED; + } + if ((fp_stats = fopen(sim->profile_stats, "r")) == NULL) { + fprintf(stderr, "ERROR: Cannot open sample_profile\n"); + return FAILED; + } + break; + case PROCESS_MODEL: + if(set_model_qc(sim) == FAILED) + return FAILED; + + return SUCCEEDED; + break; + } + + // these happen only if we aren't using model-basedc + if (get_fastq_inf(sim, qc) == FAILED) { + return FAILED; + } + print_fastq_stats(sim, fastq); + + return SUCCEEDED; +} + +/////////////////////////////////////////////////////// +// Function: parse_options - parse the user options // +/////////////////////////////////////////////////////// + +void parse_options(int argc, char** argv, sim_t *sim) +{ + + char *tp, *tmp_buf; + long len; + long num; + long ratio; unsigned int seed = (unsigned int)time(NULL); // Variables for Option @@ -187,6 +243,8 @@ {"prefix", 1, NULL, 0}, {"sample-profile-id", 1, NULL, 0}, {"seed", 1, NULL, 0}, + {"help", 0, NULL, 0}, + {"version", 0, NULL, 0}, {0, 0, 0, 0} }; @@ -195,7 +253,7 @@ while ((opt = getopt_long(argc, argv, "", long_options, &option_index)) != -1) { switch (opt) { case 0: - sim.set_flg[option_index] = 1; + sim->set_flg[option_index] = 1; switch (option_index) { case 0: @@ -208,9 +266,9 @@ case 1: if (strncmp(optarg, "CLR", 3) == 0) { - sim.data_type = DATA_TYPE_CLR; + sim->data_type = DATA_TYPE_CLR; } else if (strncmp(optarg, "CCS", 3) == 0) { - sim.data_type = DATA_TYPE_CCS; + sim->data_type = DATA_TYPE_CCS; } else { fprintf(stderr, "ERROR (data-type: %s): Acceptable value is CLR or CCS.\n", optarg); exit(-1); @@ -218,81 +276,81 @@ break; case 2: - sim.depth = atof(optarg); - if (sim.depth <= 0.0) { + sim->depth = atof(optarg); + if (sim->depth <= 0.0) { fprintf(stderr, "ERROR (depth: %s): Acceptable range is more than 0.\n", optarg); exit(-1); } break; case 3: - sim.len_mean = atof(optarg); - if ((sim.len_mean < 1) || (sim.len_mean > FASTQ_LEN_MAX)) { - fprintf(stderr, "ERROR (length-mean: %s): Acceptable range is 1-%ld.\n", optarg, FASTQ_LEN_MAX); + sim->len_mean = atof(optarg); + if ((sim->len_mean < 1) || (sim->len_mean > FASTQ_LEN_MAX)) { + fprintf(stderr, "ERROR (length-mean: %s): Acceptable range is 1-%ld.\n", optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } break; case 4: - sim.len_sd = atof(optarg); - if ((sim.len_sd < 0) || (sim.len_sd > FASTQ_LEN_MAX)) { + sim->len_sd = atof(optarg); + if ((sim->len_sd < 0) || (sim->len_sd > FASTQ_LEN_MAX)) { fprintf(stderr, "ERROR (length-sd: %s): Acceptable range is 0-%ld.\n", - optarg, FASTQ_LEN_MAX); + optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } break; case 5: if (strlen(optarg) >= 8) { - fprintf(stderr, "ERROR (length-min: %s): Acceptable range is 1-%ld.\n", optarg, FASTQ_LEN_MAX); + fprintf(stderr, "ERROR (length-min: %s): Acceptable range is 1-%ld.\n", optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } - sim.len_min = atoi(optarg); - if ((sim.len_min < 1) || (sim.len_min > FASTQ_LEN_MAX)) { - fprintf(stderr, "ERROR (length-min: %s): Acceptable range is 1-%ld.\n", optarg, FASTQ_LEN_MAX); + sim->len_min = atoi(optarg); + if ((sim->len_min < 1) || (sim->len_min > FASTQ_LEN_MAX)) { + fprintf(stderr, "ERROR (length-min: %s): Acceptable range is 1-%ld.\n", optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } break; case 6: if (strlen(optarg) >= 8) { - fprintf(stderr, "ERROR (length-max: %s): Acceptable range is 1-%ld.\n", optarg, FASTQ_LEN_MAX); + fprintf(stderr, "ERROR (length-max: %s): Acceptable range is 1-%ld.\n", optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } - sim.len_max = atoi(optarg); - if ((sim.len_max < 1) || (sim.len_max > FASTQ_LEN_MAX)) { - fprintf(stderr, "ERROR (length-max: %s): Acceptable range is 1-%ld.\n", optarg, FASTQ_LEN_MAX); + sim->len_max = atoi(optarg); + if ((sim->len_max < 1) || (sim->len_max > FASTQ_LEN_MAX)) { + fprintf(stderr, "ERROR (length-max: %s): Acceptable range is 1-%ld.\n", optarg, (long)(FASTQ_LEN_MAX)); exit(-1); } break; case 7: - sim.accuracy_mean = atof(optarg); - if ((sim.accuracy_mean < 0.0) || (sim.accuracy_mean > 1.0)) { + sim->accuracy_mean = atof(optarg); + if ((sim->accuracy_mean < 0.0) || (sim->accuracy_mean > 1.0)) { fprintf(stderr, "ERROR (accuracy-mean: %s): Acceptable range is 0.0-1.0.\n", optarg); exit(-1); } break; case 8: - sim.accuracy_sd = atof(optarg); - if ((sim.accuracy_sd < 0.0) || (sim.accuracy_sd > 1.0)) { + sim->accuracy_sd = atof(optarg); + if ((sim->accuracy_sd < 0.0) || (sim->accuracy_sd > 1.0)) { fprintf(stderr, "ERROR (accuracy-sd: %s): Acceptable range is 0.0-1.0.\n", optarg); exit(-1); } break; case 9: - sim.accuracy_min = atof(optarg); - if ((sim.accuracy_min < 0.0) || (sim.accuracy_min > 1.0)) { + sim->accuracy_min = atof(optarg); + if ((sim->accuracy_min < 0.0) || (sim->accuracy_min > 1.0)) { fprintf(stderr, "ERROR (accuracy-min: %s): Acceptable range is 0.0-1.0.\n", optarg); exit(-1); } break; case 10: - sim.accuracy_max = atof(optarg); - if ((sim.accuracy_max < 0.0) || (sim.accuracy_max > 1.0)) { + sim->accuracy_max = atof(optarg); + if ((sim->accuracy_max < 0.0) || (sim->accuracy_max > 1.0)) { fprintf(stderr, "ERROR (accuracy-max: %s): Acceptable range is 0.0-1.0.\n", optarg); exit(-1); } @@ -321,45 +379,54 @@ exit(-1); } if (num == 0) { - sim.sub_ratio = ratio; + sim->sub_ratio = ratio; } else if (num == 1) { - sim.ins_ratio = ratio; + sim->ins_ratio = ratio; } else if (num == 2) { - sim.del_ratio = ratio; + sim->del_ratio = ratio; } num ++; tp = strtok(NULL, ":"); } + free(tmp_buf); break; case 12: - if ((sim.model_qc_file = (char *)malloc(strlen(optarg) + 1)) == 0) { + if ((sim->model_qc_file = (char *)malloc(strlen(optarg) + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); exit(-1); } - strcpy(sim.model_qc_file, optarg); + strcpy(sim->model_qc_file, optarg); break; case 13: - if ((sim.prefix = (char *)malloc(strlen(optarg) + 1)) == 0) { + if ((sim->prefix = (char *)malloc(strlen(optarg) + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); exit(-1); } - strcpy(sim.prefix, optarg); + strcpy(sim->prefix, optarg); break; case 14: - if ((sim.profile_id = (char *)malloc(strlen(optarg) + 1)) == 0) { + if ((sim->profile_id = (char *)malloc(strlen(optarg) + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); exit(-1); } - strcpy(sim.profile_id, optarg); + strcpy(sim->profile_id, optarg); break; case 15: seed = (unsigned int)atoi(optarg); break; + case 16: // help + print_help(); + exit(0); + + case 17: // version + printf("pbsim %s\n", versionString); + exit(0); + defalut: break; } @@ -370,209 +437,65 @@ } srand((unsigned int)seed); - - if (argv[optind] == '\0') { - print_help(); - exit(-1); - } - - // Quality code to error probability - for (i=0; i<=93; i++) { - qc[i].prob = pow(10, (double)i / -10); - qc[i].character = (char)(i+33); - } - - // Setting of simulation parameters - if (set_sim_param() == FAILED) { - exit(-1); - } - print_sim_param(); - - // FASTQ - if (sim.process == PROCESS_SAMPLING) { - if ((fp_filtered = tmpfile()) == NULL) { - fprintf(stderr, "ERROR: Cannot open temporary file\n"); - return FAILED; - } - - if (get_fastq_inf() == FAILED) { - exit(-1); - } - print_fastq_stats(); - } else if (sim.process == PROCESS_SAMPLING_STORE) { - if ((fp_filtered = fopen(sim.profile_fq, "w+")) == NULL) { - fprintf(stderr, "ERROR: Cannot open sample_profile\n"); - return FAILED; - } - if ((fp_stats = fopen(sim.profile_stats, "w+")) == NULL) { - fprintf(stderr, "ERROR: Cannot open sample_profile\n"); - return FAILED; - } - - if (get_fastq_inf() == FAILED) { - exit(-1); - } - print_fastq_stats(); - } else if (sim.process == PROCESS_SAMPLING_REUSE) { - if ((fp_filtered = fopen(sim.profile_fq, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open sample_profile\n"); - return FAILED; - } - if ((fp_stats = fopen(sim.profile_stats, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open sample_profile\n"); - return FAILED; - } - - if (get_fastq_inf() == FAILED) { - exit(-1); - } - print_fastq_stats(); - } - - // Quality code model - if (sim.process == PROCESS_MODEL) { - if (set_model_qc() == FAILED) { - exit(-1); - } - } - - // Reference sequence - if ((ref.file = (char *)malloc(strlen(argv[optind]) + 1)) == 0) { - fprintf(stderr, "ERROR: Cannot allocate memory.\n"); - exit(-1); - } - strcpy(ref.file, argv[optind]); - - if (get_ref_inf() == FAILED) { - exit(-1); - } - - // Set mutation parameters and varianeces - if (set_mut() == FAILED) { - exit(-1); - } - - // Creating simulated reads - for (ref.num=1; ref.num<=ref.num_seq; ref.num++) { - if (get_ref_seq() == FAILED) { - exit(-1); - } - - init_sim_res(); - - sprintf(sim.outfile_fq, "%s_%04d.fastq", sim.prefix, ref.num); - if ((fp_fq = fopen(sim.outfile_fq, "w")) == NULL) { - fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim.outfile_fq); - return FAILED; - } - - sprintf(sim.outfile_maf, "%s_%04d.maf", sim.prefix, ref.num); - if ((fp_maf = fopen(sim.outfile_maf, "w")) == NULL) { - fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim.outfile_maf); - return FAILED; - } - - sim.len_quota = (long long)(sim.depth * ref.len); - - if (sim.process == PROCESS_MODEL) { - if (simulate_by_model() == FAILED) { - exit(-1); - } - } else { - if (simulate_by_sampling() == FAILED) { - exit(-1); - } - } - - print_simulation_stats(); - - fclose(fp_fq); - fclose(fp_maf); - } - - if ((sim.process == PROCESS_SAMPLING_STORE) || (sim.process == PROCESS_SAMPLING_REUSE)) { - fclose(fp_filtered); - fclose(fp_stats); - } - - rst2 = get_time_cpu(); - t2 = get_time(); - - fprintf(stderr, ":::: System utilization ::::\n\n"); - fprintf(stderr, "CPU time(s) : %d\n", rst2 - rst1); - fprintf(stderr, "Elapsed time(s) : %d\n", t2 - t1); - - return(0); -} - -/////////////////////////////////////// -// Function: trim - Remove "\n" // -/////////////////////////////////////// - -int trim(char *line) { - int end_pos = strlen(line) - 1; - - if (line[end_pos] == '\n') { - line[end_pos] = '\0'; - return 1; - } - return 0; } /////////////////////////////////////////////////////// // Function: get_ref_inf - Get reference information // /////////////////////////////////////////////////////// -int get_ref_inf() { +int get_ref_inf(const sim_t *sim, ref_t *ref) { FILE *fp; char line[BUF_SIZE]; - int ret; long max_len = 0; + int ret; fprintf(stderr, ":::: Reference stats ::::\n\n"); - fprintf(stderr, "file name : %s\n", ref.file); + fprintf(stderr, "file name : %s\n", ref->file); fprintf(stderr, "\n"); - if ((fp = fopen(ref.file, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open file: %s\n", ref.file); + if ((fp = fopen(ref->file, "r")) == NULL) { + fprintf(stderr, "ERROR: Cannot open reference file: %s\n", ref->file); return FAILED; } - ref.num_seq = 0; - ref.len = 0; + ref->num_seq = 0; + ref->len = 0; while (fgets(line, BUF_SIZE, fp) != NULL) { ret = trim(line); if (line[0] == '>') { - if (ref.num_seq != 0) { - if (ref.len < REF_SEQ_LEN_MIN) { - fprintf(stderr, "ERROR: Reference is too short. Acceptable length >= %ld.\n", REF_SEQ_LEN_MIN); + if (ref->num_seq != 0) { + if (ref->len < REF_SEQ_LEN_MIN) { + fprintf(stderr, "ERROR: Reference is too short. Acceptable length >= %ld.\n", (long)(REF_SEQ_LEN_MIN)); + fclose(fp); return FAILED; } - fprintf(stderr, "ref.%d (len:%d) : %s\n", ref.num_seq, ref.len, ref.id); + fprintf(stderr, "ref.%ld (len:%ld) : %s\n", ref->num_seq, ref->len, ref->id); fclose(fp_ref); - if (ref.len > max_len) { - max_len = ref.len; + if (ref->len > max_len) { + max_len = ref->len; } } - ref.num_seq ++; - if (ref.num_seq > REF_SEQ_NUM_MAX) { - fprintf(stderr, "ERROR: References are too many. Max number of reference is %ld.\n", REF_SEQ_NUM_MAX); + ref->num_seq ++; + if (ref->num_seq > REF_SEQ_NUM_MAX) { + fprintf(stderr, "ERROR: References are too many. Max number of reference is %ld.\n", (long)(REF_SEQ_NUM_MAX)); + fclose(fp); return FAILED; } - strncpy(ref.id, line + 1, REF_ID_LEN_MAX); - ref.id[REF_ID_LEN_MAX] = '\0'; + strncpy(ref->id, &line[1], REF_ID_LEN_MAX); + ref->id[std::min(REF_ID_LEN_MAX, (int)strlen(&line[1]))] = '\0'; - sprintf(sim.outfile_ref, "%s_%04d.ref", sim.prefix, ref.num_seq); - if ((fp_ref = fopen(sim.outfile_ref, "w")) == NULL) { - fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim.outfile_ref); + sprintf(sim->outfile_ref, "%s_%04ld.ref", sim->prefix, ref->num_seq); + if ((fp_ref = fopen(sim->outfile_ref, "w")) == NULL) { + fprintf(stderr, "ERROR: Cannot open output file: %s\n", sim->outfile_ref); + fclose(fp); return FAILED; } - ref.len = 0; + ref->len = 0; while (ret != EXISTS_LINE_FEED) { if (fgets(line, BUF_SIZE, fp) == NULL) { @@ -581,12 +504,13 @@ ret = trim(line); } - fprintf(fp_ref, ">%s\n", ref.id); + fprintf(fp_ref, ">%s\n", ref->id); } else { - ref.len += strlen(line); + ref->len += strlen(line); - if (ref.len > REF_SEQ_LEN_MAX) { - fprintf(stderr, "ERROR: Reference is too long. Acceptable length <= %ld.\n", REF_SEQ_LEN_MAX); + if (ref->len > REF_SEQ_LEN_MAX) { + fprintf(stderr, "ERROR: Reference is too long. Acceptable length <= %ld.\n", (long)(REF_SEQ_LEN_MAX)); + fclose(fp); return FAILED; } @@ -595,19 +519,19 @@ } fclose(fp); - if (ref.len < REF_SEQ_LEN_MIN) { - fprintf(stderr, "ERROR: Reference is too short. Acceptable length >= %ld.\n", REF_SEQ_LEN_MIN); + if (ref->len < REF_SEQ_LEN_MIN) { + fprintf(stderr, "ERROR: Reference is too short. Acceptable length >= %ld.\n", (long)(REF_SEQ_LEN_MIN)); return FAILED; } - fprintf(stderr, "ref.%d (len:%d) : %s\n", ref.num_seq, ref.len, ref.id); + fprintf(stderr, "ref.%ld (len:%ld) : %s\n", ref->num_seq, ref->len, ref->id); fclose(fp_ref); - if (ref.len > max_len) { - max_len = ref.len; + if (ref->len > max_len) { + max_len = ref->len; } fprintf(stderr, "\n"); - if ((ref.seq = (char *)malloc(max_len + 1)) == 0) { + if ((ref->seq = (char *)malloc(max_len + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } @@ -619,17 +543,17 @@ // Function: get_ref_seq - Get reference sequence // //////////////////////////////////////////////////// -int get_ref_seq() { +int get_ref_seq(const sim_t *sim, ref_t *ref) { FILE *fp; char line[BUF_SIZE]; long offset = 0; long copy_size; int ret; - sprintf(sim.outfile_ref, "%s_%04d.ref", sim.prefix, ref.num); + sprintf(sim->outfile_ref, "%s_%04ld.ref", sim->prefix, ref->num); - if ((fp = fopen(sim.outfile_ref, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open file: %s\n", sim.outfile_ref); + if ((fp = fopen(sim->outfile_ref, "r")) == NULL) { + fprintf(stderr, "ERROR: Cannot open outfile_ref file: %s\n", sim->outfile_ref); return FAILED; } @@ -637,6 +561,8 @@ ret = trim(line); if (line[0] == '>') { + memcpy(ref->id, &line[1], strlen(line)-1); + ref->id[std::min(REF_ID_LEN_MAX, (int)strlen(&line[1]))] = '\0'; while (ret != EXISTS_LINE_FEED) { if (fgets(line, BUF_SIZE, fp) == NULL) { break; @@ -645,14 +571,14 @@ } } else { copy_size = strlen(line); - memcpy(ref.seq + offset, line, copy_size); + memcpy(ref->seq + offset, line, copy_size); offset += copy_size; } } fclose(fp); - ref.seq[offset] = '\0'; - ref.len = strlen(ref.seq); + ref->seq[offset] = '\0'; + ref->len = strlen(ref->seq); return SUCCEEDED; } @@ -661,7 +587,7 @@ // Function: get_fastq_inf - Get FASTQ information // ///////////////////////////////////////////////////// -int get_fastq_inf() { +int get_fastq_inf(const sim_t *sim, const qc_t *qc) { FILE *fp; char *tp, *item; char line[BUF_SIZE]; @@ -675,7 +601,7 @@ long i; int line_num; - for (i=0; i<=sim.len_max; i++) { + for (i=0; i<=sim->len_max; i++) { freq_len[i] = 0; } for (i=0; i<=100000; i++) { @@ -691,7 +617,7 @@ fastq.len_max_filtered = 0; fastq.len_total_filtered = 0; - if (sim.process == PROCESS_SAMPLING_REUSE) { + if (sim->process == PROCESS_SAMPLING_REUSE) { while (fgets(line, BUF_SIZE, fp_stats) != NULL) { trim(line); tp = strtok(line, "\t"); @@ -718,7 +644,7 @@ } } else { if ((fp = fopen(fastq.file, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open file: %s\n", fastq.file); + fprintf(stderr, "ERROR: Cannot open fastq file: %s\n", fastq.file); return FAILED; } @@ -734,7 +660,8 @@ len += strlen(line); if (len > FASTQ_LEN_MAX) { - fprintf(stderr, "ERROR: fastq is too long. Max acceptable length is %ld.\n", FASTQ_LEN_MAX); + fprintf(stderr, "ERROR: fastq is too long. Max acceptable length is %ld.\n", (long)(FASTQ_LEN_MAX)); + fclose(fp); return FAILED; } @@ -742,7 +669,8 @@ fastq.len_total += len; if (fastq.num > FASTQ_NUM_MAX) { - fprintf(stderr, "ERROR: fastq is too many. Max acceptable number is %ld.\n", FASTQ_NUM_MAX); + fprintf(stderr, "ERROR: fastq is too many. Max acceptable number is %ld.\n", (long)(FASTQ_NUM_MAX)); + fclose(fp); return FAILED; } @@ -753,7 +681,7 @@ fastq.len_min = len; } - if ((len >= sim.len_min) && (len <= sim.len_max)) { + if ((len >= sim->len_min) && (len <= sim->len_max)) { strcat(qc_tmp, line); prob = 0.0; for (i=0; i= sim.accuracy_min) && (accuracy <= sim.accuracy_max)) { + if ((accuracy >= sim->accuracy_min) && (accuracy <= sim->accuracy_max)) { accuracy_total += accuracy; fastq.num_filtered ++; fastq.len_total_filtered += len; freq_len[len] ++; - value = (int)(accuracy * 100000 + 0.5); + value = (int)(accuracy * 100000 + 0.5); freq_accuracy[value] ++; fprintf(fp_filtered, "%s\n", qc_tmp); @@ -789,7 +717,8 @@ if (line_num == 3) { len += strlen(line); if (len > FASTQ_LEN_MAX) { - fprintf(stderr, "ERROR: fastq is too long. Max acceptable length is %ld.\n", FASTQ_LEN_MAX); + fprintf(stderr, "ERROR: fastq is too long. Max acceptable length is %ld.\n", (long)(FASTQ_LEN_MAX)); + fclose(fp); return FAILED; } strcat(qc_tmp, line); @@ -808,8 +737,8 @@ fastq.accuracy_mean_filtered = accuracy_total / fastq.num_filtered; variance = 0.0; - for (i=0; i<=sim.len_max; i++) { - if (freq_len[i] > 0) { + for (i=0; i<=sim->len_max; i++) { + if (freq_len[i] > 0) { variance += pow((fastq.len_mean_filtered - i), 2) * freq_len[i]; } } @@ -817,15 +746,15 @@ variance = 0.0; for (i=0; i<=100000; i++) { - if (freq_accuracy[i] > 0) { + if (freq_accuracy[i] > 0) { variance += pow((fastq.accuracy_mean_filtered - i * 0.00001), 2) * freq_accuracy[i]; } } fastq.accuracy_sd_filtered = sqrt(variance / fastq.num_filtered); - if (sim.process == PROCESS_SAMPLING_STORE) { + if (sim->process == PROCESS_SAMPLING_STORE) { fprintf(fp_stats, "num\t%ld\n", fastq.num_filtered); - fprintf(fp_stats, "len_total\t%ld\n", fastq.len_total_filtered); + fprintf(fp_stats, "len_total\t%lld\n", fastq.len_total_filtered); fprintf(fp_stats, "len_min\t%ld\n", fastq.len_min_filtered); fprintf(fp_stats, "len_max\t%ld\n", fastq.len_max_filtered); fprintf(fp_stats, "len_mean\t%f\n", fastq.len_mean_filtered); @@ -838,217 +767,175 @@ return SUCCEEDED; } -///////////////////////////////////////////////////// -// Function: print_fastq_stats - Print FASTQ stats // -///////////////////////////////////////////////////// - -void print_fastq_stats() { - fprintf(stderr, ":::: FASTQ stats ::::\n\n"); - - if (sim.process == PROCESS_SAMPLING_REUSE) { - fprintf(stderr, "file name : %s\n", sim.profile_fq); - } else { - fprintf(stderr, "file name : %s\n", fastq.file); - fprintf(stderr, "\n:: all reads ::\n"); - fprintf(stderr, "read num. : %ld\n", fastq.num); - fprintf(stderr, "read total length : %lld\n", fastq.len_total); - fprintf(stderr, "read min length : %ld\n", fastq.len_min); - fprintf(stderr, "read max length : %ld\n", fastq.len_max); - } - - fprintf(stderr, "\n:: filtered reads ::\n"); - fprintf(stderr, "read num. : %ld\n", fastq.num_filtered); - fprintf(stderr, "read total length : %lld\n", fastq.len_total_filtered); - fprintf(stderr, "read min length : %ld\n", fastq.len_min_filtered); - fprintf(stderr, "read max length : %ld\n", fastq.len_max_filtered); - fprintf(stderr, "read length mean (SD) : %f (%f)\n", - fastq.len_mean_filtered, fastq.len_sd_filtered); - fprintf(stderr, "read accuracy mean (SD) : %f (%f)\n", - fastq.accuracy_mean_filtered, fastq.accuracy_sd_filtered); - fprintf(stderr, "\n"); -} - ////////////////////////////////////////////////////////// // Function: init_sim_res - Initiate simulation results // ////////////////////////////////////////////////////////// -void init_sim_res() { - sim.res_num = 0; - sim.res_len_total = 0; - sim.res_sub_num = 0; - sim.res_ins_num = 0; - sim.res_del_num = 0; - sim.res_len_min = LONG_MAX; - sim.res_len_max = 0; +void init_sim_res(sim_t *sim) { + sim->res_num = 0; + sim->res_len_total = 0; + sim->res_sub_num = 0; + sim->res_ins_num = 0; + sim->res_del_num = 0; + sim->res_len_min = LONG_MAX; + sim->res_len_max = 0; } ///////////////////////////////////////////////////////// // Function: set_sim_param - Set simulation parameters // ///////////////////////////////////////////////////////// -int set_sim_param() { +int set_sim_param(sim_t *sim) { FILE *fp; long sum; // data-type - if (!(sim.set_flg[1])) { - sim.data_type = DATA_TYPE_CLR; + if (!(sim->set_flg[1])) { + sim->data_type = DATA_TYPE_CLR; } // depth - if (!(sim.set_flg[2])) { - sim.depth = (sim.data_type == DATA_TYPE_CLR) ? 20.0 : 50.0; + if (!(sim->set_flg[2])) { + sim->depth = (sim->data_type == DATA_TYPE_CLR) ? 20.0 : 50.0; } // length-mean - if (!(sim.set_flg[3])) { - sim.len_mean = (sim.data_type == DATA_TYPE_CLR) ? 3000 : 450; + if (!(sim->set_flg[3])) { + sim->len_mean = (sim->data_type == DATA_TYPE_CLR) ? 3000 : 450; } // length-sd - if (!(sim.set_flg[4])) { - sim.len_sd = (sim.data_type == DATA_TYPE_CLR) ? 2300 : 170; + if (!(sim->set_flg[4])) { + sim->len_sd = (sim->data_type == DATA_TYPE_CLR) ? 2300 : 170; } // length-min - if (!(sim.set_flg[5])) { - sim.len_min = (sim.data_type == DATA_TYPE_CLR) ? 100 : 100; + if (!(sim->set_flg[5])) { + sim->len_min = (sim->data_type == DATA_TYPE_CLR) ? 100 : 100; } // length-max - if (!(sim.set_flg[6])) { - sim.len_max = (sim.data_type == DATA_TYPE_CLR) ? 25000 : 2500; + if (!(sim->set_flg[6])) { + sim->len_max = (sim->data_type == DATA_TYPE_CLR) ? 25000 : 2500; } // accuracy-mean - if (sim.data_type == DATA_TYPE_CLR) { - if (sim.set_flg[7]) { - sim.accuracy_mean = int(sim.accuracy_mean * 100) * 0.01; + if (sim->data_type == DATA_TYPE_CLR) { + if (sim->set_flg[7]) { + sim->accuracy_mean = int(sim->accuracy_mean * 100) * 0.01; } else { - sim.accuracy_mean = 0.78; + sim->accuracy_mean = 0.78; } } else { - sim.accuracy_mean = 0.98; + sim->accuracy_mean = 0.98; } // accuracy-sd - if (sim.data_type == DATA_TYPE_CLR) { - if (sim.set_flg[8]) { - sim.accuracy_sd = int(sim.accuracy_sd * 100) * 0.01; - } else { - sim.accuracy_sd = 0.02; - } + if (sim->data_type == DATA_TYPE_CLR && sim->set_flg[8]) { + sim->accuracy_sd = int(sim->accuracy_sd * 100) * 0.01; } else { - sim.accuracy_sd = 0.02; + sim->accuracy_sd = 0.02; } // accuracy-min - if (sim.data_type == DATA_TYPE_CLR) { - if (sim.set_flg[9]) { - sim.accuracy_min = int(sim.accuracy_min * 100) * 0.01; - } else { - sim.accuracy_min = 0.75; - } + if (sim->data_type == DATA_TYPE_CLR && sim->set_flg[9]) { + sim->accuracy_min = int(sim->accuracy_min * 100) * 0.01; } else { - sim.accuracy_min = 0.75; + sim->accuracy_min = 0.75; } // accuracy-max - if (sim.data_type == DATA_TYPE_CLR) { - if (sim.set_flg[10]) { - sim.accuracy_max = int(sim.accuracy_max * 100) * 0.01; - } else { - sim.accuracy_max = 1.0; - } + if (sim->data_type == DATA_TYPE_CLR && sim->set_flg[10]) { + sim->accuracy_max = int(sim->accuracy_max * 100) * 0.01; } else { - sim.accuracy_max = 1.0; + sim->accuracy_max = 1.0; } // difference-ratio - if (!(sim.set_flg[11])) { - if (sim.data_type == DATA_TYPE_CLR) { - sim.sub_ratio = 10; - sim.ins_ratio = 60; - sim.del_ratio = 30; + if (!(sim->set_flg[11])) { + if (sim->data_type == DATA_TYPE_CLR) { + sim->sub_ratio = 10; + sim->ins_ratio = 60; + sim->del_ratio = 30; } else { - sim.sub_ratio = 6; - sim.ins_ratio = 21; - sim.del_ratio = 73; + sim->sub_ratio = 6; + sim->ins_ratio = 21; + sim->del_ratio = 73; } } - sum = sim.sub_ratio + sim.ins_ratio + sim.del_ratio; - sim.sub_rate = (double)sim.sub_ratio / sum; - sim.ins_rate = (double)sim.ins_ratio / sum; - sim.del_rate = (double)sim.del_ratio / sum; + sum = sim->sub_ratio + sim->ins_ratio + sim->del_ratio; + sim->sub_rate = (double)sim->sub_ratio / sum; + sim->ins_rate = (double)sim->ins_ratio / sum; + sim->del_rate = (double)sim->del_ratio / sum; // prefix and outfile - if (!(sim.set_flg[13])) { - if ((sim.prefix = (char *)malloc(3)) == 0) { + if (!(sim->set_flg[13])) { + if ((sim->prefix = (char *)malloc(3)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); exit(-1); } - strcpy(sim.prefix, "sd"); + strcpy(sim->prefix, "sd"); } - if ((sim.outfile_ref = (char *)malloc(strlen(sim.prefix) + 10)) == 0) { + if ((sim->outfile_ref = (char *)malloc(strlen(sim->prefix) + 10)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((sim.outfile_fq = (char *)malloc(strlen(sim.prefix) + 12)) == 0) { + if ((sim->outfile_fq = (char *)malloc(strlen(sim->prefix) + 12)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((sim.outfile_maf = (char *)malloc(strlen(sim.prefix) + 10)) == 0) { + if ((sim->outfile_maf = (char *)malloc(strlen(sim->prefix) + 10)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } // profile - if (sim.set_flg[14]) { - if ((sim.profile_fq = (char *)malloc(strlen(sim.profile_id) + 22)) == 0) { + if (sim->set_flg[14]) { + if ((sim->profile_fq = (char *)malloc(strlen(sim->profile_id) + 22)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((sim.profile_stats = (char *)malloc(strlen(sim.profile_id) + 22)) == 0) { + if ((sim->profile_stats = (char *)malloc(strlen(sim->profile_id) + 22)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - sprintf(sim.profile_fq, "sample_profile_%s.fastq", sim.profile_id); - sprintf(sim.profile_stats, "sample_profile_%s.stats", sim.profile_id); + sprintf(sim->profile_fq, "sample_profile_%s.fastq", sim->profile_id); + sprintf(sim->profile_stats, "sample_profile_%s.stats", sim->profile_id); } // length and accuracy - if (sim.len_min > sim.len_max) { - fprintf(stderr, "ERROR: length min(%ld) is greater than max(%ld).\n", sim.len_min, sim.len_max); + if (sim->len_min > sim->len_max) { + fprintf(stderr, "ERROR: length min(%ld) is greater than max(%ld).\n", sim->len_min, sim->len_max); return FAILED; } - if (sim.accuracy_min > sim.accuracy_max) { - fprintf(stderr, "ERROR: accuracy min(%f) is greater than max(%f).\n", sim.accuracy_min, sim.accuracy_max); + if (sim->accuracy_min > sim->accuracy_max) { + fprintf(stderr, "ERROR: accuracy min(%f) is greater than max(%f).\n", sim->accuracy_min, sim->accuracy_max); return FAILED; } // process - if (sim.set_flg[12]) { - if ((sim.set_flg[0]) || (sim.set_flg[14])) { + if (sim->set_flg[12]) { + if ((sim->set_flg[0]) || (sim->set_flg[14])) { fprintf(stderr, "ERROR: either --sample-fastq(and/or --sample-profile-id)(sampling-based) or --model_qc(model-based) should be set.\n"); return FAILED; } - sim.process = PROCESS_MODEL; + sim->process = PROCESS_MODEL; } else { - if (sim.set_flg[0]) { - if (sim.set_flg[14]) { - sim.process = PROCESS_SAMPLING_STORE; + if (sim->set_flg[0]) { + if (sim->set_flg[14]) { + sim->process = PROCESS_SAMPLING_STORE; } else { - sim.process = PROCESS_SAMPLING; + sim->process = PROCESS_SAMPLING; } } else { - if (sim.set_flg[14]) { - sim.process = PROCESS_SAMPLING_REUSE; + if (sim->set_flg[14]) { + sim->process = PROCESS_SAMPLING_REUSE; } else { fprintf(stderr, "ERROR: either --sample-fastq(and/or --sample-profile-id)(sampling-based) or --model_qc(model-based) should be set.\n"); return FAILED; @@ -1057,27 +944,27 @@ } // sample profile - if (sim.process == PROCESS_SAMPLING_STORE) { - if ((fp = fopen(sim.profile_fq, "r")) != NULL) { - fprintf(stderr, "ERROR: %s exists.\n", sim.profile_fq); + if (sim->process == PROCESS_SAMPLING_STORE) { + if ((fp = fopen(sim->profile_fq, "r")) != NULL) { + fprintf(stderr, "ERROR: %s exists.\n", sim->profile_fq); fclose(fp); return FAILED; } - if ((fp = fopen(sim.profile_stats, "r")) != NULL) { - fprintf(stderr, "ERROR: %s exists.\n", sim.profile_stats); + if ((fp = fopen(sim->profile_stats, "r")) != NULL) { + fprintf(stderr, "ERROR: %s exists.\n", sim->profile_stats); fclose(fp); return FAILED; } } - if (sim.process == PROCESS_SAMPLING_REUSE) { - if ((fp = fopen(sim.profile_fq, "r")) == NULL) { - fprintf(stderr, "ERROR: %s does not exist.\n", sim.profile_fq); + if (sim->process == PROCESS_SAMPLING_REUSE) { + if ((fp = fopen(sim->profile_fq, "r")) == NULL) { + fprintf(stderr, "ERROR: %s does not exist.\n", sim->profile_fq); return FAILED; } fclose(fp); - if ((fp = fopen(sim.profile_stats, "r")) == NULL) { - fprintf(stderr, "ERROR: %s does not exist.\n", sim.profile_stats); + if ((fp = fopen(sim->profile_stats, "r")) == NULL) { + fprintf(stderr, "ERROR: %s does not exist.\n", sim->profile_stats); return FAILED; } fclose(fp); @@ -1090,7 +977,7 @@ // Function: simulate_by_sampling - Simulate by model // //////////////////////////////////////////////////////// -int simulate_by_sampling() { +int simulate_by_sampling(sim_t *sim, ref_t *ref, mut_t *mut, fastq_t *fastq, qc_t *qc) { long len; long long len_total = 0; long sampling_num, sampling_interval, sampling_value, sampling_residue; @@ -1103,7 +990,7 @@ char id[128]; int digit_num1[4], digit_num2[4], digit_num[4]; - for (i=0; i<=sim.len_max; i++) { + for (i=0; i<=sim->len_max; i++) { freq_len[i] = 0; } for (i=0; i<=100000; i++) { @@ -1111,33 +998,33 @@ } for (i=0; i<=93; i++) { - mut.sub_thre[i] = int((qc[i].prob * sim.sub_rate) * 1000000 + 0.5); - mut.ins_thre[i] = int((qc[i].prob * (sim.sub_rate + sim.ins_rate)) * 1000000 + 0.5); + mut->sub_thre[i] = int((qc[i].prob * sim->sub_rate) * 1000000 + 0.5); + mut->ins_thre[i] = int((qc[i].prob * (sim->sub_rate + sim->ins_rate)) * 1000000 + 0.5); } - mut.del_thre = int((1.0 - fastq.accuracy_mean_filtered) * sim.del_rate * 1000000 + 0.5); + mut->del_thre = int((1.0 - fastq->accuracy_mean_filtered) * sim->del_rate * 1000000 + 0.5); - sampling_num = (long)(sim.len_quota / fastq.len_total_filtered); - sampling_residue = sim.len_quota % fastq.len_total_filtered; + sampling_num = (long)(sim->len_quota / fastq->len_total_filtered); + sampling_residue = sim->len_quota % fastq->len_total_filtered; if (sampling_residue == 0) { sampling_interval = 1; } else { - sampling_interval = (long)((double)(fastq.len_total_filtered / sampling_residue) * 2 + 0.5); - if (sampling_interval > (long)(fastq.num_filtered * 0.5)) { - sampling_interval = (long)(fastq.num_filtered * 0.5); + sampling_interval = (long)((double)(fastq->len_total_filtered / sampling_residue) * 2 + 0.5); + if (sampling_interval > (long)(fastq->num_filtered * 0.5)) { + sampling_interval = (long)(fastq->num_filtered * 0.5); } } // Make simulation data - while (len_total < sim.len_quota) { + while (len_total < sim->len_quota) { rewind(fp_filtered); - sampling_value = rand() % fastq.num_filtered; - while (fgets(mut.qc, fastq.len_max_filtered + 2, fp_filtered) != NULL) { - if (len_total >= sim.len_quota) { + sampling_value = rand() % fastq->num_filtered; + while (fgets(mut->qc, fastq->len_max_filtered + 2, fp_filtered) != NULL) { + if (len_total >= sim->len_quota) { break; } - trim(mut.qc); + trim(mut->qc); if (sampling_value % sampling_interval == 0) { num = sampling_num + 1; @@ -1147,77 +1034,77 @@ sampling_value ++; for (i=0; i= sim.len_quota) { + if (len_total >= sim->len_quota) { break; } - mut.tmp_len_max = sim.len_quota - len_total; - if (mut.tmp_len_max < sim.len_min) { - mut.tmp_len_max = sim.len_min; + mut->tmp_len_max = sim->len_quota - len_total; + if (mut->tmp_len_max < sim->len_min) { + mut->tmp_len_max = sim->len_min; } - if (mutate() == FAILED) { + if (mutate(sim, ref) == FAILED) { return FAILED; } - sim.res_num ++; - len = strlen(mut.new_seq); - sim.res_len_total += len; + sim->res_num ++; + len = strlen(mut->new_seq); + sim->res_len_total += len; len_total += len; freq_len[len] ++; - if (len > sim.res_len_max) { - sim.res_len_max = len; + if (len > sim->res_len_max) { + sim->res_len_max = len; } - if (len < sim.res_len_min) { - sim.res_len_min = len; + if (len < sim->res_len_min) { + sim->res_len_min = len; } prob = 0.0; for (j=0; jnew_qc[j] - 33].prob; } accuracy = 1.0 - (prob / len); accuracy_total += accuracy; value = (int)(accuracy * 100000 + 0.5); freq_accuracy[value] ++; - sprintf(id, "S%ld_%ld", ref.num, sim.res_num); - fprintf(fp_fq, "@%s\n%s\n+%s\n%s\n", id, mut.new_seq, id, mut.new_qc); + sprintf(id, "S%ld_%ld", ref->num, sim->res_num); + fprintf(fp_fq, "@%s\n%s\n+%s\n%s\n", id, mut->new_seq, id, mut->new_qc); digit_num1[0] = 3; - digit_num2[0] = 1 + count_digit(sim.res_num); + digit_num2[0] = 1 + count_digit(sim->res_num); digit_num[0] = (digit_num1[0] >= digit_num2[0]) ? digit_num1[0] : digit_num2[0]; - digit_num1[1] = count_digit((mut.seq_left - 1)); + digit_num1[1] = count_digit((mut->seq_left - 1)); digit_num2[1] = 1; digit_num[1] = (digit_num1[1] >= digit_num2[1]) ? digit_num1[1] : digit_num2[1]; - digit_num1[2] = count_digit((mut.seq_right - mut.seq_left + 1)); + digit_num1[2] = count_digit((mut->seq_right - mut->seq_left + 1)); digit_num2[2] = count_digit(len); digit_num[2] = (digit_num1[2] >= digit_num2[2]) ? digit_num1[2] : digit_num2[2]; - digit_num1[3] = count_digit(ref.len); + digit_num1[3] = count_digit(ref->len); digit_num2[3] = count_digit(len); digit_num[3] = (digit_num1[3] >= digit_num2[3]) ? digit_num1[3] : digit_num2[3]; - fprintf(fp_maf, "a\ns ref"); + fprintf(fp_maf, "a\ns ref"); while (digit_num1[0] ++ < digit_num[0]) { fprintf(fp_maf, " "); } while (digit_num1[1] ++ < digit_num[1]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d", mut.seq_left - 1); + fprintf(fp_maf, " %ld", mut->seq_left - 1); while (digit_num1[2] ++ < digit_num[2]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d +", mut.seq_right - mut.seq_left + 1); + fprintf(fp_maf, " %ld +", mut->seq_right - mut->seq_left + 1); while (digit_num1[3] ++ < digit_num[3]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %s\n", ref.len, mut.maf_ref_seq); - fprintf(fp_maf, "s %s", id); + fprintf(fp_maf, " %ld %s\n", ref->len, mut->maf_ref_seq); + fprintf(fp_maf, "s %s", id); while (digit_num2[0] ++ < digit_num[0]) { fprintf(fp_maf, " "); } @@ -1228,39 +1115,39 @@ while (digit_num2[2] ++ < digit_num[2]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %c", len, mut.seq_strand); + fprintf(fp_maf, " %ld %c", len, mut->seq_strand); while (digit_num2[3] ++ < digit_num[3]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %s\n\n", len, mut.maf_seq); + fprintf(fp_maf, " %ld %s\n\n", len, mut->maf_seq); } } sampling_num = 0; } - sim.res_len_mean = (double)sim.res_len_total / sim.res_num; - sim.res_accuracy_mean = accuracy_total / sim.res_num; + sim->res_len_mean = (double)sim->res_len_total / sim->res_num; + sim->res_accuracy_mean = accuracy_total / sim->res_num; - if (sim.res_num == 1) { - sim.res_len_sd = 0.0; - sim.res_accuracy_sd = 0.0; + if (sim->res_num == 1) { + sim->res_len_sd = 0.0; + sim->res_accuracy_sd = 0.0; } else { variance = 0.0; - for (i=0; i<=sim.len_max; i++) { + for (i=0; i<=sim->len_max; i++) { if (freq_len[i] > 0) { - variance += pow((sim.res_len_mean - i), 2) * freq_len[i]; + variance += pow((sim->res_len_mean - i), 2) * freq_len[i]; } } - sim.res_len_sd = sqrt(variance / sim.res_num); + sim->res_len_sd = sqrt(variance / sim->res_num); variance = 0.0; for (i=0; i<=100000; i++) { if (freq_accuracy[i] > 0) { - variance += pow((sim.res_accuracy_mean - i * 0.00001), 2) * freq_accuracy[i]; + variance += pow((sim->res_accuracy_mean - i * 0.00001), 2) * freq_accuracy[i]; } } - sim.res_accuracy_sd = sqrt(variance / sim.res_num); + sim->res_accuracy_sd = sqrt(variance / sim->res_num); } return SUCCEEDED; @@ -1270,7 +1157,7 @@ // Function: simulate_by_model - Simulate by Model // ///////////////////////////////////////////////////// -int simulate_by_model() { +int simulate_by_model(sim_t *sim, ref_t *ref, qc_t *qc) { long len; long long len_total = 0; long num; @@ -1287,7 +1174,7 @@ char id[128]; int digit_num1[4], digit_num2[4], digit_num[4]; - for (i=0; i<=sim.len_max; i++) { + for (i=0; i<=sim->len_max; i++) { freq_len[i] = 0; } for (i=0; i<=100000; i++) { @@ -1295,26 +1182,26 @@ } for (i=0; i<=93; i++) { - mut.sub_thre[i] = int((qc[i].prob * sim.sub_rate) * 1000000 + 0.5); - mut.ins_thre[i] = int((qc[i].prob * (sim.sub_rate + sim.ins_rate)) * 1000000 + 0.5); + mut.sub_thre[i] = int((qc[i].prob * sim->sub_rate) * 1000000 + 0.5); + mut.ins_thre[i] = int((qc[i].prob * (sim->sub_rate + sim->ins_rate)) * 1000000 + 0.5); } - mut.del_thre = int((1.0 - sim.accuracy_mean) * sim.del_rate * 1000000 + 0.5); + mut.del_thre = int((1.0 - sim->accuracy_mean) * sim->del_rate * 1000000 + 0.5); - accuracy_min = (long)(sim.accuracy_min * 100); - accuracy_max = (long)(sim.accuracy_max * 100); + accuracy_min = (long)(sim->accuracy_min * 100); + accuracy_max = (long)(sim->accuracy_max * 100); // length distribution - variance = log(1 + pow((sim.len_sd / sim.len_mean) ,2)); - mean = log(sim.len_mean) - variance * 0.5; + variance = log(1 + pow((sim->len_sd / sim->len_mean) ,2)); + mean = log(sim->len_mean) - variance * 0.5; sd = sqrt(variance); - if (sim.len_sd == 0.0) { - prob2len[1] = int(sim.len_mean + 0.5); + if (sim->len_sd == 0.0) { + prob2len[1] = int(sim->len_mean + 0.5); len_rand_value = 1; } else { - start_wk = 1; + start_wk = 1; len_prob_total = 0.0; - for (i=sim.len_min; i<=sim.len_max; i++) { + for (i=sim->len_min; i<=sim->len_max; i++) { len_prob_total += exp(-1 * pow((log(i)-mean), 2) / 2 / variance) / sqrt(2*M_PI) / sd / i; end_wk = int(len_prob_total * 100000 + 0.5); if (end_wk > 100000) { @@ -1339,16 +1226,16 @@ } // accuracy distribution - if (sim.data_type == DATA_TYPE_CLR) { - mean = sim.accuracy_mean * 100; - sd = sim.accuracy_sd * 100; + if (sim->data_type == DATA_TYPE_CLR) { + mean = sim->accuracy_mean * 100; + sd = sim->accuracy_sd * 100; variance = pow(sd, 2); if (sd == 0.0) { prob2accuracy[1] = int(mean + 0.5); accuracy_rand_value = 1; } else { - start_wk = 1; + start_wk = 1; accuracy_prob_total = 0.0; for (i=accuracy_min; i<=accuracy_max; i++) { accuracy_prob_total += exp(-1 * pow(i - mean, 2) / 2 / variance) / sqrt(2 * M_PI) / sd; @@ -1374,7 +1261,7 @@ sum += exp(0.5 * (i - 75)); } - start_wk = 1; + start_wk = 1; accuracy_prob_total = 0.0; for (i=accuracy_min; i<=accuracy_max; i++) { accuracy_prob_total += exp(0.5 * (i - 75)) / sum; @@ -1402,7 +1289,7 @@ // quality code distributiin for (i=accuracy_min; i<=accuracy_max; i++) { - start_wk = 1; + start_wk = 1; qc_prob_total = 0.0; for (j=model_qc[i].min; j<=model_qc[i].max; j++) { @@ -1425,14 +1312,14 @@ } // simulation - while (len_total < sim.len_quota) { + while (len_total < sim->len_quota) { index = rand() % len_rand_value + 1; len = prob2len[index]; - if (len_total + len > sim.len_quota) { - len = sim.len_quota - len_total; + if (len_total + len > sim->len_quota) { + len = sim->len_quota - len_total; - if (len < sim.len_min) { - len = sim.len_min; + if (len < sim->len_min) { + len = sim->len_min; } } @@ -1452,21 +1339,21 @@ } mut.qc[num] = '\0'; - if (mutate() == FAILED) { + if (mutate(sim, ref) == FAILED) { return FAILED; } len = strlen(mut.new_seq); - sim.res_len_total += len; + sim->res_len_total += len; len_total += len; freq_len[len] ++; - sim.res_num ++; + sim->res_num ++; - if (len > sim.res_len_max) { - sim.res_len_max = len; + if (len > sim->res_len_max) { + sim->res_len_max = len; } - if (len < sim.res_len_min) { - sim.res_len_min = len; + if (len < sim->res_len_min) { + sim->res_len_min = len; } prob = 0.0; @@ -1478,11 +1365,11 @@ accuracy = (int)(value * 100000 + 0.5); freq_accuracy[accuracy] ++; - sprintf(id, "S%ld_%ld", ref.num, sim.res_num); + sprintf(id, "S%ld_%ld", ref->num, sim->res_num); fprintf(fp_fq, "@%s\n%s\n+%s\n%s\n", id, mut.new_seq, id, mut.new_qc); digit_num1[0] = 3; - digit_num2[0] = 1 + count_digit(sim.res_num); + digit_num2[0] = 1 + count_digit(sim->res_num); digit_num[0] = (digit_num1[0] >= digit_num2[0]) ? digit_num1[0] : digit_num2[0]; digit_num1[1] = count_digit((mut.seq_left - 1)); @@ -1493,26 +1380,26 @@ digit_num2[2] = count_digit(len); digit_num[2] = (digit_num1[2] >= digit_num2[2]) ? digit_num1[2] : digit_num2[2]; - digit_num1[3] = count_digit(ref.len); + digit_num1[3] = count_digit(ref->len); digit_num2[3] = count_digit(len); digit_num[3] = (digit_num1[3] >= digit_num2[3]) ? digit_num1[3] : digit_num2[3]; - fprintf(fp_maf, "a\ns ref"); + fprintf(fp_maf, "a\ns %s", ref->id); while (digit_num1[0] ++ < digit_num[0]) { fprintf(fp_maf, " "); } while (digit_num1[1] ++ < digit_num[1]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d", mut.seq_left - 1); + fprintf(fp_maf, " %ld", mut.seq_left - 1); while (digit_num1[2] ++ < digit_num[2]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d +", mut.seq_right - mut.seq_left + 1); + fprintf(fp_maf, " %ld +", mut.seq_right - mut.seq_left + 1); while (digit_num1[3] ++ < digit_num[3]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %s\n", ref.len, mut.maf_ref_seq); + fprintf(fp_maf, " %ld %s\n", ref->len, mut.maf_ref_seq); fprintf(fp_maf, "s %s", id); while (digit_num2[0] ++ < digit_num[0]) { fprintf(fp_maf, " "); @@ -1524,135 +1411,83 @@ while (digit_num2[2] ++ < digit_num[2]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %c", len, mut.seq_strand); + fprintf(fp_maf, " %ld %c", len, mut.seq_strand); while (digit_num2[3] ++ < digit_num[3]) { fprintf(fp_maf, " "); } - fprintf(fp_maf, " %d %s\n\n", len, mut.maf_seq); + fprintf(fp_maf, " %ld %s\n\n", len, mut.maf_seq); } - sim.res_len_mean = (double)sim.res_len_total / sim.res_num; - sim.res_accuracy_mean = accuracy_total / sim.res_num; + sim->res_len_mean = (double)sim->res_len_total / sim->res_num; + sim->res_accuracy_mean = accuracy_total / sim->res_num; - if (sim.res_num == 1) { - sim.res_len_sd = 0.0; - sim.res_accuracy_sd = 0.0; + if (sim->res_num == 1) { + sim->res_len_sd = 0.0; + sim->res_accuracy_sd = 0.0; } else { variance = 0.0; - for (i=0; i<=sim.len_max; i++) { + for (i=0; i<=sim->len_max; i++) { if (freq_len[i] > 0) { - variance += pow((sim.res_len_mean - i), 2) * freq_len[i]; + variance += pow((sim->res_len_mean - i), 2) * freq_len[i]; } } - sim.res_len_sd = sqrt(variance / sim.res_num); + sim->res_len_sd = sqrt(variance / sim->res_num); variance = 0.0; for (i=0; i<=100000; i++) { if (freq_accuracy[i] > 0) { - variance += pow((sim.res_accuracy_mean - i * 0.00001), 2) * freq_accuracy[i]; + variance += pow((sim->res_accuracy_mean - i * 0.00001), 2) * freq_accuracy[i]; } } - sim.res_accuracy_sd = sqrt(variance / sim.res_num); + sim->res_accuracy_sd = sqrt(variance / sim->res_num); } return SUCCEEDED; } -///////////////////////////////////////////////////////////// -// Function: print_sim_param - Print simulation parameters // -///////////////////////////////////////////////////////////// - -void print_sim_param() { - fprintf(stderr, ":::: Simulation parameters :::\n\n"); - - if (sim.process == PROCESS_MODEL) { - fprintf(stderr, "Simulated by stochastic model.\n\n"); - } else { - fprintf(stderr, "Simulated by fastq sampling.\n\n"); - } - - fprintf(stderr, "prefix : %s\n", sim.prefix); - if (sim.set_flg[14]) { - fprintf(stderr, "sample_profile_id : %s\n", sim.profile_id); - } - - if (sim.data_type == DATA_TYPE_CLR) { - fprintf(stderr, "data-type : CLR\n"); - } else { - fprintf(stderr, "data-type : CCS\n"); - } - - fprintf(stderr, "depth : %lf\n", sim.depth); - - if (sim.set_flg[0]) { - fprintf(stderr, "length-mean : (sampling FASTQ)\n"); - fprintf(stderr, "length-sd : (sampling FASTQ)\n"); - } else { - fprintf(stderr, "length-mean : %f\n", sim.len_mean); - fprintf(stderr, "length-sd : %f\n", sim.len_sd); - } - fprintf(stderr, "length-min : %ld\n", sim.len_min); - fprintf(stderr, "length-max : %ld\n", sim.len_max); - - if (sim.set_flg[0]) { - fprintf(stderr, "accuracy-mean : (sampling FASTQ)\n"); - fprintf(stderr, "accuracy-sd : (sampling FASTQ)\n"); - } else { - fprintf(stderr, "accuracy-mean : %f\n", sim.accuracy_mean); - fprintf(stderr, "accuracy-sd : %f\n", sim.accuracy_sd); - } - fprintf(stderr, "accuracy-min : %f\n", sim.accuracy_min); - fprintf(stderr, "accuracy-max : %f\n", sim.accuracy_max); - - fprintf(stderr, "difference-ratio : %d:%d:%d\n", - sim.sub_ratio, sim.ins_ratio, sim.del_ratio); - - fprintf(stderr, "\n"); -} - ///////////////////////////////////////////////////////////////// // Function: set_mut - Set mutation parameters and varianeces // ///////////////////////////////////////////////////////////////// -int set_mut() { - mut.sub_nt_a = "TGC"; - mut.sub_nt_t = "AGC"; - mut.sub_nt_g = "ATC"; - mut.sub_nt_c = "ATG"; - mut.sub_nt_n = "ATGC"; - mut.ins_nt = "ATGC"; +int set_mut(sim_t *sim) { + mut.sub_nt_a = (char *)"TGC"; + mut.sub_nt_t = (char *)"AGC"; + mut.sub_nt_g = (char *)"ATC"; + mut.sub_nt_c = (char *)"ATG"; + mut.sub_nt_n = (char *)"ATGC"; + mut.ins_nt = (char *)"ATGC"; - if ((mut.qc = (char *)malloc(sim.len_max + 1)) == 0) { + if ((mut.qc = (char *)malloc(sim->len_max + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.new_qc = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.new_qc = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.tmp_qc = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.tmp_qc = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.seq = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.seq = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.new_seq = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.new_seq = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.maf_seq = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.maf_seq = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } - if ((mut.maf_ref_seq = (char *)malloc(sim.len_max * 2 + 1)) == 0) { + if ((mut.maf_ref_seq = (char *)malloc(sim->len_max * 2 + 1)) == 0) { fprintf(stderr, "ERROR: Cannot allocate memory.\n"); return FAILED; } @@ -1664,7 +1499,7 @@ // Function: mutate - Mutate read // //////////////////////////////////// -int mutate() { +int mutate(sim_t *sim, ref_t *ref) { char *line; char nt; long num; @@ -1686,7 +1521,7 @@ mut.tmp_qc[offset ++] = mut.qc[i]; if (rand() % 1000000 < mut.del_thre) { mut.tmp_qc[offset ++] = ' '; - sim.res_del_num ++; + sim->res_del_num ++; } } mut.tmp_qc[offset ++] = mut.qc[len - 1]; @@ -1694,28 +1529,28 @@ len = strlen(mut.tmp_qc); - if (len >= ref.len) { + if (len >= ref->len) { offset = 0; - len = ref.len; + len = ref->len; } else { - offset = rand() % (ref.len - len + 1); + offset = rand() % (ref->len - len + 1); } mut.seq_left = offset + 1; mut.seq_right = offset + len; - if (sim.res_num % 2 == 0) { + if (sim->res_num % 2 == 0) { mut.seq_strand = '+'; for (i=0; iseq[offset + i]); mut.seq[i] = nt; } } else { mut.seq_strand = '-'; for (i=0; iseq[offset + i]); if (nt == 'A') { mut.seq[len-1-i] = 'T'; @@ -1752,7 +1587,7 @@ qc_value = (int)mut.tmp_qc[i] - 33; if (rand_value < mut.sub_thre[qc_value]) { - sim.res_sub_num ++; + sim->res_sub_num ++; index = rand() % 3; if (nt == 'A') { mut.new_seq[offset] = mut.sub_nt_a[index]; @@ -1768,7 +1603,7 @@ } mut.maf_ref_seq[maf_offset] = nt; } else if (rand_value < mut.ins_thre[qc_value]) { - sim.res_ins_num ++; + sim->res_ins_num ++; index = rand() % 8; if (index >= 4) { mut.new_seq[offset] = nt; @@ -1803,36 +1638,11 @@ return SUCCEEDED; } -//////////////////////////////////////////////////////////////// -// Function: print_simulation_stats - Print Simulation Stats. // -//////////////////////////////////////////////////////////////// - -void print_simulation_stats() { - sim.res_depth = (double)sim.res_len_total / ref.len; - sim.res_sub_rate = (double)sim.res_sub_num / sim.res_len_total; - sim.res_ins_rate = (double)sim.res_ins_num / sim.res_len_total; - sim.res_del_rate = (double)sim.res_del_num / sim.res_len_total; - - fprintf(stderr, ":::: Simulation stats (ref.%d) ::::\n\n", ref.num); - fprintf(stderr, "read num. : %ld\n", sim.res_num); - fprintf(stderr, "depth : %lf\n", sim.res_depth); - fprintf(stderr, "read length mean (SD) : %f (%f)\n", - sim.res_len_mean, sim.res_len_sd); - fprintf(stderr, "read length min : %ld\n", sim.res_len_min); - fprintf(stderr, "read length max : %ld\n", sim.res_len_max); - fprintf(stderr, "read accuracy mean (SD) : %f (%f)\n", - sim.res_accuracy_mean, sim.res_accuracy_sd); - fprintf(stderr, "substitution rate. : %f\n", sim.res_sub_rate); - fprintf(stderr, "insertion rate. : %f\n", sim.res_ins_rate); - fprintf(stderr, "deletion rate. : %f\n", sim.res_del_rate); - fprintf(stderr, "\n"); -} - /////////////////////////////////////////////////////// // Function: set_model_qc - Set quality code model // /////////////////////////////////////////////////////// -int set_model_qc() { +int set_model_qc(const sim_t *sim) { FILE *fp; char line[BUF_SIZE]; char *tp; @@ -1840,8 +1650,8 @@ int num; int i, j; - if ((fp = fopen(sim.model_qc_file, "r")) == NULL) { - fprintf(stderr, "ERROR: Cannot open file: %s\n", sim.model_qc_file); + if ((fp = fopen(sim->model_qc_file, "r")) == NULL) { + fprintf(stderr, "ERROR: Cannot open model_qc file: %s\n", sim->model_qc_file); return FAILED; } @@ -1887,122 +1697,3 @@ return SUCCEEDED; } - -/////////////////////////////////////////////////////// -// Function: get_time_cpu - Get CPU time // -/////////////////////////////////////////////////////// - -long get_time_cpu() { - struct rusage ru; - getrusage(RUSAGE_SELF, &ru); - return ru.ru_utime.tv_sec; -} - -/////////////////////////////////////////////////////// -// Function: get_time - Get time // -/////////////////////////////////////////////////////// - -long get_time() { - struct timeval tv; - gettimeofday(&tv, NULL); - return tv.tv_sec; -} - -/////////////////////////////////////// -// Function: print_help - Print help // -/////////////////////////////////////// - -void print_help() { - fprintf(stderr, "\n"); - fprintf(stderr, "USAGE: pbsim [options] \n\n"); - fprintf(stderr, " FASTA format file.\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " [general options]\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " --prefix prefix of output files (sd).\n"); - fprintf(stderr, " --data-type data type. CLR or CCS (CLR).\n"); - fprintf(stderr, " --depth depth of coverage (CLR: 20.0, CCS: 50.0).\n"); - fprintf(stderr, " --length-min minimum length (100).\n"); - fprintf(stderr, " --length-max maximum length (CLR: 25000, CCS: 2500).\n"); - fprintf(stderr, " --accuracy-min minimum accuracy.\n"); - fprintf(stderr, " (CLR: 0.75, CCS: fixed as 0.75).\n"); - fprintf(stderr, " this option can be used only in case of CLR.\n"); - fprintf(stderr, " --accuracy-max maximum accuracy.\n"); - fprintf(stderr, " (CLR: 1.00, CCS: fixed as 1.00).\n"); - fprintf(stderr, " this option can be used only in case of CLR.\n"); - fprintf(stderr, " --difference-ratio ratio of differences. substitution:insertion:deletion.\n"); - fprintf(stderr, " each value up to 1000 (CLR: 10:60:30, CCS:6:21:73).\n"); - fprintf(stderr, " --seed for a pseudorandom number generator (Unix time).\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " [options of sampling-based simulation]\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " --sample-fastq FASTQ format file to sample.\n"); - fprintf(stderr, " --sample-profile-id sample-fastq (filtered) profile ID.\n"); - fprintf(stderr, " when using --sample-fastq, profile is stored.\n"); - fprintf(stderr, " 'sample_profile_.fastq', and\n"); - fprintf(stderr, " 'sample_profile_.stats' are created.\n"); - fprintf(stderr, " when not using --sample-fastq, profile is re-used.\n"); - fprintf(stderr, " Note that when profile is used, --length-min,max,\n"); - fprintf(stderr, " --accuracy-min,max would be the same as the profile.\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " [options of model-based simulation].\n"); - fprintf(stderr, "\n"); - fprintf(stderr, " --model_qc model of quality code.\n"); - fprintf(stderr, " --length-mean mean of length model (CLR: 3000.0, CCS:450.0).\n"); - fprintf(stderr, " --length-sd standard deviation of length model.\n"); - fprintf(stderr, " (CLR: 2300.0, CCS: 170.0).\n"); - fprintf(stderr, " --accuracy-mean mean of accuracy model.\n"); - fprintf(stderr, " (CLR: 0.78, CCS: fixed as 0.98).\n"); - fprintf(stderr, " this option can be used only in case of CLR.\n"); - fprintf(stderr, " --accuracy-sd standard deviation of accuracy model.\n"); - fprintf(stderr, " (CLR: 0.02, CCS: fixed as 0.02).\n"); - fprintf(stderr, " this option can be used only in case of CLR.\n"); - fprintf(stderr, "\n"); -} - -///////////////////////////////////////// -// Function: count_digit - count digit // -///////////////////////////////////////// - -int count_digit(long num) { - int digit = 1; - int quotient; - - quotient = int(num / 10); - - while (quotient != 0) { - digit ++; - quotient = int(quotient / 10); - } - - return digit; -} - -////////////////////////////////////////////////////// -// Function: revcomp - convert to reverse complement// -////////////////////////////////////////////////////// - -void revcomp(char* str) { - int i, len; - char c; - - len = strlen(str); - - for(i=0; i