diff -Nru libhmsbeagle-2.1.2+20171110/debian/changelog libhmsbeagle-2.1.2+git20180307/debian/changelog --- libhmsbeagle-2.1.2+20171110/debian/changelog 2018-02-23 08:08:56.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/debian/changelog 2018-04-11 12:02:53.000000000 +0000 @@ -1,3 +1,13 @@ +libhmsbeagle (2.1.2+git20180307-1) unstable; urgency=medium + + * New Github commit + * d/watch now scans Github commits (deleted get-orig-source) + * Standards-Version: 4.1.4 + * Point Vcs fields to salsa.debian.org + * Remove unused lintian override + + -- Andreas Tille Wed, 11 Apr 2018 14:02:53 +0200 + libhmsbeagle (2.1.2+20171110-1) unstable; urgency=medium * New upstream version diff -Nru libhmsbeagle-2.1.2+20171110/debian/control libhmsbeagle-2.1.2+git20180307/debian/control --- libhmsbeagle-2.1.2+20171110/debian/control 2018-02-23 08:08:56.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/debian/control 2018-04-11 12:02:53.000000000 +0000 @@ -15,9 +15,9 @@ ocl-icd-opencl-dev | opencl-dev, pocl-opencl-icd [amd64] | opencl-icd [amd64], clinfo -Standards-Version: 4.1.3 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libhmsbeagle.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/libhmsbeagle.git +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/libhmsbeagle +Vcs-Git: https://salsa.debian.org/med-team/libhmsbeagle.git Homepage: https://github.com/beagle-dev/beagle-lib Package: libhmsbeagle-dev diff -Nru libhmsbeagle-2.1.2+20171110/debian/copyright libhmsbeagle-2.1.2+git20180307/debian/copyright --- libhmsbeagle-2.1.2+20171110/debian/copyright 2018-02-23 08:08:56.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/debian/copyright 2018-04-11 12:02:53.000000000 +0000 @@ -2,6 +2,11 @@ Upstream-Name: beagle-lib Upstream-Contact: Marc Suchard Source: https://github.com/beagle-dev/beagle-lib.git +Files-Excluded: */project + */epochtest + */.gitignore + */.dirstamp + */.deps Files: * Copyright: 2009-2015 The BEAGLE Developer group diff -Nru libhmsbeagle-2.1.2+20171110/debian/get-orig-source libhmsbeagle-2.1.2+git20180307/debian/get-orig-source --- libhmsbeagle-2.1.2+20171110/debian/get-orig-source 2018-02-23 08:08:56.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/debian/get-orig-source 1970-01-01 00:00:00.000000000 +0000 @@ -1,49 +0,0 @@ -#!/bin/sh - -COMPRESS=xz - -set -e - -NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` -MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'` - -mkdir -p ../tarballs -cd ../tarballs -# need to clean up the tarballs dir first because upstream tarball might -# contain a directory with unpredictable name -rm -rf * -git clone --quiet https://github.com/beagle-dev/beagle-lib.git -cd beagle-lib -VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d` -# for esthetical reasons set file timestamps (if git-restore-mtime is installed) -git restore-mtime || true -cd .. -TARDIR=${NAME}-${VERSION} -mv beagle-lib ${TARDIR} -rm -rf ${TARDIR}/.git -# remove binaries -find . -name epochtest -type f -delete -find . -name .dirstamp -type f -delete -find . -name .cproject -type f -delete -find . -name .project -type f -delete -find . -name "*.isl" -type f -delete -find . -name "*.isproj" -type f -delete -find . -name "*.props" -type f -delete -find . -name "*.vcxproj*" -type f -delete -find . -name "*.exe" -type f -delete -find . -name "*.bat" -type f -delete -find . -name "*.sln" -type f -delete -find . -name .dirs -type d | xargs rm -rf -find . -type d -empty | xargs rm -rf -rm -rf ${TARDIR}/project - -GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" -rm -rf ${TARDIR} - -cat < - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAAGTGAGGTACACACGATTCATAAGATACCGAGAGGGACGTGGGATCATGTCCGTTGGAGGCATGCTCAACTGGCGTAAGTGGTAAACTGGATGTCTCTAGTAGTGGGCAAGCGTCGTGAGGCGCAAAAGTACTTGTGGTAAGGACCAGAGATGCACAGGCTATCTTCTTTAATCTAATGCGATACTCGTTGAAGTCTATCTTTGAGATAGCTAAGATCACATAGGGACTTTGATAGCCAACAGTGTGCATGGCACTGTAATAATTTTTTGGCAGACCACACTTGGGTGGGGAGAGTAGAGAAAGTGAATCGATGAGCAGGTTCCGCGGCTGGGGGGGTTAGGGATATCACAAGATTGTCTCTTAAACACGGGGTTTAGGGTTACTTACAAGAAGATGAATGCCGGAGCAGGGGGTCATCTTAAGGAATCGGGGAATTTGTCCTCGGGCAAGAATTGACACCTGCCTCATTATTATTCATGAGACTACAAAAAGGGGATAGTTGAATTACATTAGCGCGCGGTCGAACTCCGACTGAAAATAATAAGCGTAAATGGAACCCAGCCACAGTGACTGGTAAGCAAATGTTTAGTTTAAACAACCAGGGTAATGGTGCATTTCAGAAACTGGGGACAAGTCGATTACGGCGGTTGATTACCGGGTCCTGTTAGGTGTAGGGAGCCCATCTACTGGCACATTTTTTTGTGCGTATCGACGGGGACCCAGTGAAAAGGAGTAACTGATAAAGTACAGTGAATGAATAATGTAAAAGCGGGACGAGTAAAAGCATACATAGTGCGTGAAAGGTGTCAGTTTACCTACCTGGGACAATCTCTGTACGTGAGTAAGTTTGGATCCAGCGGAAAACCACAGGTGAGAGGGCTTCTGAAACGCATGCCCGATTAGATAACTGATAATGTAAACCAGGACGCTTCAGCTGTGAATGCCTGTATAAAATCCCTGGGTTTTCAGGAATGGAAATAACGCTGACCAGCTATT - - - - - ATAAAAAAGGGGTGCAAAAGAACACGTGCAATTAAAATAAGGCCGGTCGATGTATAAGGTTACATCGCCAGTGAGTTATCTGGATCAATCTTGTTTCTTCTTAGAAAACGAAACATCTAAAGAGTTCATTGAGGAGTATGGCGGAGTTTATGGGATGGTTCTCGATCTTCTGCAGACACGAGAAGCAGCAGCAAAACTATATGATCAAGCGAATGAAGATAAAATTGGGGATTGATCAATGGGGGCTGCATACGGACTTGCACCATAGTAAGCAGCTAACGTGTCATAATAATGGTGATTAGAAGAGTAGGTTAGTGAGAATTAATAATCGGCGGAAATTGGGATTATACCTTATGCTGGCGCCGATAAGAGGTAATGAGTGACACAAATAAAGGGTAAATATAATCGGACGGAGCGTAATTCGGAGAGACTAATGGACGGGATGTAAAGTTCACACTAGGACTGTAACTGTTGGAACGTAAGAAAAAATCGAGAAGGAGCAAATGGGGTATAGGATGTACCGCAAGGTCTTACATTAAAAAGACGAAGTGGATGGCGGGTCTGAGTGAACAGGTTGTTCATTTGGGACGATGACCAGGTTATGGAACCAATAAGAAGTTATAGTAGAACAGGATAAATCCACAGAATTTCATCATGAGAGAGTTAAAATGACTATGGCGGCCCTATCTGTGGCAGAGAAACCATTAACTCGCCAGTGAATTCTCCTTGCGAGGCTGGGAGCATCAGCGTGAGACGAACAAAGATTGCATCGGTTAGATAAAACCAGTAATGCGTATCAGACCAAGTGTGTCAAAGAGTTTATTCAGAGGGCGGGACACATGGATCTAAGATCAGCTCGACCGGCGGATTCCAGTTAGTGGAGATATGCGGGGCTCTTATTGAATGGGTCCATCAGTGGTTATGGAGAAATTCGATTAACAGTAATCTTCAGGCGAGATGTGTGATCCTTTCAAACGGACAGAAGCGCGAGGTAAAATCC - - - - - ACAGGGTGCGAACCCGAGAGAATTGATAAAATCCAAATGGGTATGGTGGGTATGAACAAATGAATCATAAATAAATCGTCTGCATCGAGTTTATCCCTCGTTTGATGGCGCGGAGTTCAACAACTTATTGATCAGAAAAGGGAGAATTTGTGAGACCGCAGTTCTCTTCCTACCAGAGCAGAATGCATTGACCAAGCTCCATACGCACACAAACCCCTTTGTGATCGGGAATTGATCACAAAACGTCATACAGGAAGTAGCCTCGTCATCGGCAATCAATAGAAAAAGACCACAAGGAACGGAAGGGAAGTTCAAGGAAGAATAAGAGTAGTAAGGAACGATGTGTATATTGGTAAATTACGGCAACCAGAAGCGATGAGCCGTGCGTTCATAAGACAGACGCTATGGAACGGGGCATGACCTGGAGAGACTAATGATTAGTATATAGAATCCGACCAAGCGTGGTGGCCATTCTAATATGAGGAGACGTTGAGAAAAATGAGCCAGGAAGGGTAGCATGCCAGAAAACTCTATGCAGGAAGTAATTTAGACATATCCCTTCTGGTGCAGTAATTTGCTTATCCAAGACATTGATTCGACTCTGGGGGTCACATGGTGGTCTCATGGAATGACGAGGACTCACCGGACTATACTTGAACATAGGTGAGACAATCATGACGAATTCGCCCAAGGCGGTGCTGTTATTAGTATTGGACCGGTATCGCTGCACAAATTCAAGTAGATCGTTTGGGGGAGGATTAGGGTCACCCGGAATGAGCAATTGCGTGAATAAGAAACCCACTGAACTCGGAAGATTGATAGTTTAGTGGGTCGGATCTGTACGCTCTGGCAGAGCTCAGTTAGGAGACTTCAAAAGGAAGAATCCTACGCTTCGCCTGCGAGGTTAGGCAGATATGGGGAATGAGATGTTTCAGGTGATAATAGCTTGATGACACAAAATTAAGTCATCCCAAATCAGCAGGCAAACAGAGCAGAGCAC - - - - - - - - - - -(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981); - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Newick Tree: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ln L = - - - - diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/.config/depcomp libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/.config/depcomp --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/.config/depcomp 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/.config/depcomp 1970-01-01 00:00:00.000000000 +0000 @@ -1,630 +0,0 @@ -#! /bin/sh -# depcomp - compile a program generating dependencies as side-effects - -scriptversion=2009-04-28.21; # UTC - -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 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, see . - -# 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. Try \`$0 --help' for more information." 1>&2 - exit 1; - ;; - -h | --h*) - cat <<\EOF -Usage: depcomp [--help] [--version] PROGRAM [ARGS] - -Run PROGRAMS ARGS to compile a file, generating dependencies -as side-effects. - -Environment variables: - depmode Dependency tracking mode. - source Source file read by `PROGRAMS ARGS'. - object Object file output by `PROGRAMS ARGS'. - DEPDIR directory where to store dependencies. - depfile Dependency file to output. - tmpdepfile Temporary file to use when outputing dependencies. - libtool Whether libtool is used (yes/no). - -Report bugs to . -EOF - exit $? - ;; - -v | --v*) - echo "depcomp $scriptversion" - exit $? - ;; -esac - -if test -z "$depmode" || test -z "$source" || test -z "$object"; then - echo "depcomp: Variables source, object and depmode must be set" 1>&2 - exit 1 -fi - -# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. -depfile=${depfile-`echo "$object" | - sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} -tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} - -rm -f "$tmpdepfile" - -# Some modes work just like other modes, but use different flags. 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Hmm. -## Unfortunately, FreeBSD c89 acceptance of flags depends upon -## the command line argument order; so add the flags where they -## appear in depend2.am. Note that the slowdown incurred here -## affects only configure: in makefiles, %FASTDEP% shortcuts this. - for arg - do - case $arg in - -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; - *) set fnord "$@" "$arg" ;; - esac - shift # fnord - shift # $arg - done - "$@" - stat=$? - if test $stat -eq 0; then : - else - rm -f "$tmpdepfile" - exit $stat - fi - mv "$tmpdepfile" "$depfile" - ;; - -gcc) -## There are various ways to get dependency output from gcc. Here's -## why we pick this rather obscure method: -## - Don't want to use -MD because we'd like the dependencies to end -## up in a subdir. Having to rename by hand is ugly. -## (We might end up doing this anyway to support other compilers.) -## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like -## -MM, not -M (despite what the docs say). -## - Using -M directly means running the compiler twice (even worse -## than renaming). - if test -z "$gccflag"; then - gccflag=-MD, - fi - "$@" -Wp,"$gccflag$tmpdepfile" - stat=$? - if test $stat -eq 0; then : - else - rm -f "$tmpdepfile" - exit $stat - fi - rm -f "$depfile" - echo "$object : \\" > "$depfile" - alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz -## The second -e expression handles DOS-style file names with drive letters. - sed -e 's/^[^:]*: / /' \ - -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" -## This next piece of magic avoids the `deleted header file' problem. -## The problem is that when a header file which appears in a .P file -## is deleted, the dependency causes make to die (because there is -## typically no way to rebuild the header). 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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-time-zone: "UTC" -# time-stamp-end: "; # UTC" -# End: diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/configure.ac libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/configure.ac --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/configure.ac 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/configure.ac 1970-01-01 00:00:00.000000000 +0000 @@ -1,15 +0,0 @@ -# this is a very basic configuration example -AC_INIT([EpochTest C++], [0.1], [bug-report@hello.beagle-gpu.com], - [hellobeagle], [http://hello.beagle-gpu.com/]) -AC_PREREQ([2.59]) -AC_CONFIG_AUX_DIR(.config) -AM_INIT_AUTOMAKE([1.10 -Wall no-define]) -AC_CONFIG_HEADERS([config.h]) -AC_PROG_CXX - -PKG_CHECK_MODULES(DEPS, hmsbeagle-1 >= 1.0.0) -AC_SUBST(DEPS_CFLAGS) -AC_SUBST(DEPS_LIBS) - -AC_CONFIG_FILES([Makefile]) -AC_OUTPUT diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/COPYING libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/COPYING --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/COPYING 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/COPYING 1970-01-01 00:00:00.000000000 +0000 @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Run -`configure --help' for more details. - diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/Makefile.am libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/Makefile.am --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/Makefile.am 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/Makefile.am 1970-01-01 00:00:00.000000000 +0000 @@ -1,9 +0,0 @@ -AUTOMAKE_OPTIONS = subdir-objects -ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS} - -bin_PROGRAMS = epochtest -epochtest_SOURCES = src/epochtest.cpp -epochtest_CXXFLAGS = $(DEPS_CFLAGS) -epochtest_LDADD = $(DEPS_LIBS) - -dist_noinst_SCRIPTS = autogen.sh diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/README libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/README --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/README 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/README 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -To start editing as Eclipse project: - -(1)./autoconf.sh -(2)./configure -(3) Import to Your workspace as an existing Eclipse project - - diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/src/.deps/epochtest-epochtest.Po libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/src/.deps/epochtest-epochtest.Po --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/src/.deps/epochtest-epochtest.Po 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/src/.deps/epochtest-epochtest.Po 1970-01-01 00:00:00.000000000 +0000 @@ -1,328 +0,0 @@ -src/epochtest-epochtest.o: src/epochtest.cpp \ - /usr/local/include/libhmsbeagle-1/libhmsbeagle/beagle.h \ - /usr/local/include/libhmsbeagle-1/libhmsbeagle/platform.h \ - /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \ - /usr/include/x86_64-linux-gnu/sys/cdefs.h \ - /usr/include/x86_64-linux-gnu/bits/wordsize.h \ - /usr/include/x86_64-linux-gnu/gnu/stubs.h \ - /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ - /usr/include/c++/4.4/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.4.6/include/stddef.h \ - /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.4.6/include/stdarg.h \ - /usr/include/x86_64-linux-gnu/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.4/cctype \ - /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ - /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ - /usr/include/x86_64-linux-gnu/bits/endian.h \ - /usr/include/x86_64-linux-gnu/bits/byteswap.h \ - /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/x86_64-linux-gnu/bits/sched.h \ - /usr/include/x86_64-linux-gnu/bits/time.h \ - /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ - /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/x86_64-linux-gnu/bits/posix_opt.h \ - /usr/include/x86_64-linux-gnu/bits/environments.h \ - /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ - /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/vector \ - /usr/include/c++/4.4/bits/stl_construct.h \ - /usr/include/c++/4.4/bits/stl_uninitialized.h \ - /usr/include/c++/4.4/bits/stl_vector.h \ - /usr/include/c++/4.4/bits/stl_bvector.h \ - /usr/include/c++/4.4/bits/vector.tcc /usr/include/string.h \ - /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ - /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ - /usr/include/x86_64-linux-gnu/bits/stdio.h /usr/include/stdlib.h \ - /usr/include/x86_64-linux-gnu/bits/waitflags.h \ - /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ - /usr/include/x86_64-linux-gnu/sys/types.h \ - /usr/include/x86_64-linux-gnu/sys/select.h \ - /usr/include/x86_64-linux-gnu/bits/select.h \ - /usr/include/x86_64-linux-gnu/bits/sigset.h \ - /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h - -/usr/local/include/libhmsbeagle-1/libhmsbeagle/beagle.h: - -/usr/local/include/libhmsbeagle-1/libhmsbeagle/platform.h: - -/usr/include/c++/4.4/iostream: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/x86_64-linux-gnu/bits/predefs.h: - -/usr/include/x86_64-linux-gnu/sys/cdefs.h: - -/usr/include/x86_64-linux-gnu/bits/wordsize.h: - -/usr/include/x86_64-linux-gnu/gnu/stubs.h: - 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-/usr/include/c++/4.4/bits/move.h: - -/usr/include/c++/4.4/bits/concept_check.h: - -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.4/bits/stl_iterator.h: - -/usr/include/c++/4.4/debug/debug.h: - -/usr/include/c++/4.4/bits/localefwd.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.4/clocale: - -/usr/include/locale.h: - -/usr/include/x86_64-linux-gnu/bits/locale.h: - -/usr/include/c++/4.4/cctype: - -/usr/include/ctype.h: - -/usr/include/x86_64-linux-gnu/bits/types.h: - -/usr/include/x86_64-linux-gnu/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/x86_64-linux-gnu/bits/endian.h: - -/usr/include/x86_64-linux-gnu/bits/byteswap.h: - -/usr/include/c++/4.4/bits/ios_base.h: - -/usr/include/c++/4.4/ext/atomicity.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/x86_64-linux-gnu/bits/sched.h: - -/usr/include/x86_64-linux-gnu/bits/time.h: - -/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h: - -/usr/include/x86_64-linux-gnu/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/x86_64-linux-gnu/bits/posix_opt.h: - -/usr/include/x86_64-linux-gnu/bits/environments.h: - -/usr/include/x86_64-linux-gnu/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.4/bits/locale_classes.h: - -/usr/include/c++/4.4/string: - -/usr/include/c++/4.4/bits/allocator.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.4/ext/new_allocator.h: - -/usr/include/c++/4.4/new: - -/usr/include/c++/4.4/bits/ostream_insert.h: - -/usr/include/c++/4.4/cxxabi-forced.h: - -/usr/include/c++/4.4/bits/stl_function.h: - -/usr/include/c++/4.4/backward/binders.h: - -/usr/include/c++/4.4/bits/basic_string.h: - -/usr/include/c++/4.4/initializer_list: - -/usr/include/c++/4.4/bits/basic_string.tcc: - -/usr/include/c++/4.4/bits/locale_classes.tcc: - -/usr/include/c++/4.4/streambuf: - -/usr/include/c++/4.4/bits/streambuf.tcc: - -/usr/include/c++/4.4/bits/basic_ios.h: - -/usr/include/c++/4.4/bits/locale_facets.h: - -/usr/include/c++/4.4/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.4/bits/streambuf_iterator.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.4/bits/locale_facets.tcc: - -/usr/include/c++/4.4/bits/basic_ios.tcc: - -/usr/include/c++/4.4/bits/ostream.tcc: - -/usr/include/c++/4.4/istream: - -/usr/include/c++/4.4/bits/istream.tcc: - -/usr/include/c++/4.4/vector: - -/usr/include/c++/4.4/bits/stl_construct.h: - -/usr/include/c++/4.4/bits/stl_uninitialized.h: - -/usr/include/c++/4.4/bits/stl_vector.h: - -/usr/include/c++/4.4/bits/stl_bvector.h: - -/usr/include/c++/4.4/bits/vector.tcc: - -/usr/include/string.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/x86_64-linux-gnu/bits/stdio_lim.h: - -/usr/include/x86_64-linux-gnu/bits/sys_errlist.h: - -/usr/include/x86_64-linux-gnu/bits/stdio.h: - -/usr/include/stdlib.h: - -/usr/include/x86_64-linux-gnu/bits/waitflags.h: - -/usr/include/x86_64-linux-gnu/bits/waitstatus.h: - -/usr/include/x86_64-linux-gnu/sys/types.h: - -/usr/include/x86_64-linux-gnu/sys/select.h: - -/usr/include/x86_64-linux-gnu/bits/select.h: - -/usr/include/x86_64-linux-gnu/bits/sigset.h: - -/usr/include/x86_64-linux-gnu/sys/sysmacros.h: - -/usr/include/alloca.h: diff -Nru libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/src/epochtest.cpp libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/src/epochtest.cpp --- libhmsbeagle-2.1.2+20171110/examples/standalone/epochtest/src/epochtest.cpp 2012-05-14 23:32:54.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/examples/standalone/epochtest/src/epochtest.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,358 +0,0 @@ -#include -#include -#include -#include -#include -#include - -using namespace std; - -char - *SimSeq1 = - (char*) "TCAAGTGAGGTACACACGATTCATAAGATACCGAGAGGGACGTGGGATCATGTCCGTTGGAGGCATGCTCAACTGGCGTAAGTGGTAAACTGGATGTCTCTAGTAGTGGGCAAGCGTCGTGAGGCGCAAAAGTACTTGTGGTAAGGACCAGAGATGCACAGGCTATCTTCTTTAATCTAATGCGATACTCGTTGAAGTCTATCTTTGAGATAGCTAAGATCACATAGGGACTTTGATAGCCAACAGTGTGCATGGCACTGTAATAATTTTTTGGCAGACCACACTTGGGTGGGGAGAGTAGAGAAAGTGAATCGATGAGCAGGTTCCGCGGCTGGGGGGGTTAGGGATATCACAAGATTGTCTCTTAAACACGGGGTTTAGGGTTACTTACAAGAAGATGAATGCCGGAGCAGGGGGTCATCTTAAGGAATCGGGGAATTTGTCCTCGGGCAAGAATTGACACCTGCCTCATTATTATTCATGAGACTACAAAAAGGGGATAGTTGAATTACATTAGCGCGCGGTCGAACTCCGACTGAAAATAATAAGCGTAAATGGAACCCAGCCACAGTGACTGGTAAGCAAATGTTTAGTTTAAACAACCAGGGTAATGGTGCATTTCAGAAACTGGGGACAAGTCGATTACGGCGGTTGATTACCGGGTCCTGTTAGGTGTAGGGAGCCCATCTACTGGCACATTTTTTTGTGCGTATCGACGGGGACCCAGTGAAAAGGAGTAACTGATAAAGTACAGTGAATGAATAATGTAAAAGCGGGACGAGTAAAAGCATACATAGTGCGTGAAAGGTGTCAGTTTACCTACCTGGGACAATCTCTGTACGTGAGTAAGTTTGGATCCAGCGGAAAACCACAGGTGAGAGGGCTTCTGAAACGCATGCCCGATTAGATAACTGATAATGTAAACCAGGACGCTTCAGCTGTGAATGCCTGTATAAAATCCCTGGGTTTTCAGGAATGGAAATAACGCTGACCAGCTATT"; - -char - *SimSeq2 = - (char*) "ATAAAAAAGGGGTGCAAAAGAACACGTGCAATTAAAATAAGGCCGGTCGATGTATAAGGTTACATCGCCAGTGAGTTATCTGGATCAATCTTGTTTCTTCTTAGAAAACGAAACATCTAAAGAGTTCATTGAGGAGTATGGCGGAGTTTATGGGATGGTTCTCGATCTTCTGCAGACACGAGAAGCAGCAGCAAAACTATATGATCAAGCGAATGAAGATAAAATTGGGGATTGATCAATGGGGGCTGCATACGGACTTGCACCATAGTAAGCAGCTAACGTGTCATAATAATGGTGATTAGAAGAGTAGGTTAGTGAGAATTAATAATCGGCGGAAATTGGGATTATACCTTATGCTGGCGCCGATAAGAGGTAATGAGTGACACAAATAAAGGGTAAATATAATCGGACGGAGCGTAATTCGGAGAGACTAATGGACGGGATGTAAAGTTCACACTAGGACTGTAACTGTTGGAACGTAAGAAAAAATCGAGAAGGAGCAAATGGGGTATAGGATGTACCGCAAGGTCTTACATTAAAAAGACGAAGTGGATGGCGGGTCTGAGTGAACAGGTTGTTCATTTGGGACGATGACCAGGTTATGGAACCAATAAGAAGTTATAGTAGAACAGGATAAATCCACAGAATTTCATCATGAGAGAGTTAAAATGACTATGGCGGCCCTATCTGTGGCAGAGAAACCATTAACTCGCCAGTGAATTCTCCTTGCGAGGCTGGGAGCATCAGCGTGAGACGAACAAAGATTGCATCGGTTAGATAAAACCAGTAATGCGTATCAGACCAAGTGTGTCAAAGAGTTTATTCAGAGGGCGGGACACATGGATCTAAGATCAGCTCGACCGGCGGATTCCAGTTAGTGGAGATATGCGGGGCTCTTATTGAATGGGTCCATCAGTGGTTATGGAGAAATTCGATTAACAGTAATCTTCAGGCGAGATGTGTGATCCTTTCAAACGGACAGAAGCGCGAGGTAAAATCC"; - -char - *SimSeq3 = - (char*) "ACAGGGTGCGAACCCGAGAGAATTGATAAAATCCAAATGGGTATGGTGGGTATGAACAAATGAATCATAAATAAATCGTCTGCATCGAGTTTATCCCTCGTTTGATGGCGCGGAGTTCAACAACTTATTGATCAGAAAAGGGAGAATTTGTGAGACCGCAGTTCTCTTCCTACCAGAGCAGAATGCATTGACCAAGCTCCATACGCACACAAACCCCTTTGTGATCGGGAATTGATCACAAAACGTCATACAGGAAGTAGCCTCGTCATCGGCAATCAATAGAAAAAGACCACAAGGAACGGAAGGGAAGTTCAAGGAAGAATAAGAGTAGTAAGGAACGATGTGTATATTGGTAAATTACGGCAACCAGAAGCGATGAGCCGTGCGTTCATAAGACAGACGCTATGGAACGGGGCATGACCTGGAGAGACTAATGATTAGTATATAGAATCCGACCAAGCGTGGTGGCCATTCTAATATGAGGAGACGTTGAGAAAAATGAGCCAGGAAGGGTAGCATGCCAGAAAACTCTATGCAGGAAGTAATTTAGACATATCCCTTCTGGTGCAGTAATTTGCTTATCCAAGACATTGATTCGACTCTGGGGGTCACATGGTGGTCTCATGGAATGACGAGGACTCACCGGACTATACTTGAACATAGGTGAGACAATCATGACGAATTCGCCCAAGGCGGTGCTGTTATTAGTATTGGACCGGTATCGCTGCACAAATTCAAGTAGATCGTTTGGGGGAGGATTAGGGTCACCCGGAATGAGCAATTGCGTGAATAAGAAACCCACTGAACTCGGAAGATTGATAGTTTAGTGGGTCGGATCTGTACGCTCTGGCAGAGCTCAGTTAGGAGACTTCAAAAGGAAGAATCCTACGCTTCGCCTGCGAGGTTAGGCAGATATGGGGAATGAGATGTTTCAGGTGATAATAGCTTGATGACACAAAATTAAGTCATCCCAAATCAGCAGGCAAACAGAGCAGAGCAC"; - -void printMatrix(int matrixIndex, int stateCount, int nRateCats, int instance) { - - double* outMatrix = (double*) malloc(sizeof(double) * stateCount - * stateCount * nRateCats); - - beagleGetTransitionMatrix(instance, // instance, - matrixIndex, // matrixIndex - outMatrix // outMatrix - ); - - for (int row = 0; row < stateCount; row++) { - printf("| "); - for (int col = 0; col < stateCount; col++) - printf("%f ", outMatrix[col + row * stateCount]); - printf("|\n"); - } - printf("\n"); - - memset(outMatrix, 0, sizeof(double) * stateCount * stateCount * nRateCats); - free(outMatrix); -}//END: printMatrix - -int* getStates(char *sequence) { - int n = strlen(sequence); - int *states = (int*) malloc(sizeof(int) * n); - - for (int i = 0; i < n; i++) { - switch (sequence[i]) { - case 'A': - states[i] = 0; - break; - case 'C': - states[i] = 1; - break; - case 'G': - states[i] = 2; - break; - case 'T': - states[i] = 3; - break; - default: - states[i] = 4; - break; - } - } - return states; -}//END: getStates - -double* getPartials(char *sequence) { - int n = strlen(sequence); - double *partials = (double*) malloc(sizeof(double) * n * 4); - - int k = 0; - for (int i = 0; i < n; i++) { - switch (sequence[i]) { - case 'A': - partials[k++] = 1; - partials[k++] = 0; - partials[k++] = 0; - partials[k++] = 0; - break; - case 'C': - partials[k++] = 0; - partials[k++] = 1; - partials[k++] = 0; - partials[k++] = 0; - break; - case 'G': - partials[k++] = 0; - partials[k++] = 0; - partials[k++] = 1; - partials[k++] = 0; - break; - case 'T': - partials[k++] = 0; - partials[k++] = 0; - partials[k++] = 0; - partials[k++] = 1; - break; - default: - partials[k++] = 1; - partials[k++] = 1; - partials[k++] = 1; - partials[k++] = 1; - break; - } - } - return partials; -}//END: getPartials - -int main(int argc, const char* argv[]) { - - // is nucleotides - int stateCount = 4; - - // get the number of site patterns - int nPatterns = strlen(SimSeq1); - - int rateCategoryCount = 4; - - int nRateCats = rateCategoryCount; - int nRootCount = 1; - int nPartBuffs = 4 + nRootCount; - int scaleCount = 0; - int nConvMatBuff = 2; // number of extra transition probability matrices buffers to create - int nRateMatBuff = 6 + nConvMatBuff; - int nRateMatEigDecBuf = 2; - - // initialize the instance - BeagleInstanceDetails instDetails; - - // create an instance of the BEAGLE library - int instance = beagleCreateInstance(3, // Number of tip data elements - nPartBuffs, // Number of partials buffers to create - 0, // Number of compact state representation buffers to create - stateCount, // Number of states in the continuous-time Markov chain - nPatterns, // Number of site patterns to be handled by the instance - nRateMatEigDecBuf, // Number of rate matrix eigen-decomposition buffers to allocate - nRateMatBuff, // Number of rate matrix buffers - nRateCats, // Number of rate categories - scaleCount, // Number of scaling buffers - NULL, // List of potential resource on which this instance is allowed (NULL implies no restriction - 0, // Length of resourceList list - BEAGLE_FLAG_PROCESSOR_CPU, // Bit-flags indicating preferred implementation charactertistics, see BeagleFlags - BEAGLE_FLAG_PRECISION_DOUBLE, // Bit-flags indicating required implementation characteristics, see BeagleFlags - &instDetails); - - if (instance < 0) { - - fprintf(stderr, "Failed to obtain BEAGLE instance \n \n"); - exit(BEAGLE_ERROR_UNINITIALIZED_INSTANCE); - - } else { - - fprintf(stdout, "Using resource %i: \n", instDetails.resourceNumber); - fprintf(stdout, "\t Rsrc Name : %s \n", instDetails.resourceName); - fprintf(stdout, "\t Impl Name : %s \n", instDetails.implName); - fprintf(stdout, "\n"); - - } - - // set the sequences for each tip using partial likelihood arrays - double *SimSeq1Partials = getPartials(SimSeq1); - double *SimSeq2Partials = getPartials(SimSeq2); - double *SimSeq3Partials = getPartials(SimSeq3); - - beagleSetTipPartials(instance, 0, SimSeq3Partials); - beagleSetTipPartials(instance, 1, SimSeq2Partials); - beagleSetTipPartials(instance, 2, SimSeq1Partials); - - // alpha = 0.5 - double rates[4] = { 0.02907775442778477, 0.2807145339257214, - 0.9247730548197041, 2.76543465682679 }; - - // create base frequency array - double freqs[4] = { 0.25, 0.25, 0.25, 0.25 }; - - // create an array containing site category weights - double* weights = (double*) malloc(sizeof(double) * rateCategoryCount); - - for (int i = 0; i < rateCategoryCount; i++) { - weights[i] = 1.0 / rateCategoryCount; - } - - double* patternWeights = (double*) malloc(sizeof(double) * nPatterns); - - for (int i = 0; i < nPatterns; i++) { - patternWeights[i] = 1.0; - } - - // an eigen decomposition for the HKY kappa=1 subst model - double evecHKY1[4 * 4] = { 1.0, 2.0, 0.0, 0.5, 1.0, -2.0, 0.5, 0.0, 1.0, - 2.0, 0.0, -0.5, 1.0, -2.0, -0.5, 0.0 }; - - double ivecHKY1[4 * 4] = { 0.25, 0.25, 0.25, 0.25, 0.125, -0.125, 0.125, - -0.125, 0.0, 1.0, 0.0, -1.0, 1.0, 0.0, -1.0, 0.0 }; - - double evalHKY1[4] = { 0.0, -1.3333333333333333, -1.3333333333333333, - -1.3333333333333333 }; - - // set the Eigen decomposition for buffer 0 - beagleSetEigenDecomposition(instance, 0, evecHKY1, ivecHKY1, evalHKY1); - - // an eigen decomposition for the HKY kappa=20 subst model - double evecHKY20[4 * 4] = { 1.0, 2.0, 0.0, 0.5, 1.0, -2.0, 0.5, 0.0, 1.0, - 2.0, 0.0, -0.5, 1.0, -2.0, -0.5, 0.0 }; - - double ivecHKY20[4 * 4] = { 0.25, 0.25, 0.25, 0.25, 0.125, -0.125, 0.125, - -0.125, 0.0, 1.0, 0.0, -1.0, 1.0, 0.0, -1.0, 0.0 }; - - double evalHKY20[4] = { 0.0, -0.18181818181818182, -1.9090909084, - -1.9090909097818183 }; - - // set the Eigen decomposition for buffer 1 - beagleSetEigenDecomposition(instance, 1, evecHKY20, ivecHKY20, evalHKY20); - - beagleSetStateFrequencies(instance, 0, freqs); - - beagleSetCategoryWeights(instance, 0, weights); - - beagleSetPatternWeights(instance, patternWeights); - - double epochTransitionTimes[1] = { 20 }; - - // a list of matrix indices and edge lengths for eigen buffer 0 - int probabilityIndicesEigenBuffer0[2] = { 4, 6 }; - double edgeLengthsEigenBuffer0[2] = { epochTransitionTimes[0] - 10.0083, - epochTransitionTimes[0] }; - int listLengthEigenBuffer0 = 2; - - // a list of matrix indices and edge lengths for eigen buffer 1 - int probabilityIndicesEigenBuffer1[4] = { 1, 3, 5, 7 }; - double edgeLengthsEigenBuffer1[4] = { 25.2487, 18.48981, 45.2487 - - epochTransitionTimes[0] + 10.0083, 73.7468 - - epochTransitionTimes[0] }; - int listLengthEigenBuffer1 = 4; - - int* rootIndices = (int*) malloc(sizeof(int) * nRootCount); - int* categoryWeightsIndices = (int*) malloc(sizeof(int) * nRootCount); - int* stateFrequencyIndices = (int*) malloc(sizeof(int) * nRootCount); - int* cumulativeScalingIndices = (int*) malloc(sizeof(int) * nRootCount); - - for (int i = 0; i < nRootCount; i++) { - - rootIndices[i] = 4 + i; - categoryWeightsIndices[i] = 0; - stateFrequencyIndices[i] = 0; - cumulativeScalingIndices[i] = BEAGLE_OP_NONE; - - beagleSetCategoryRates(instance, &rates[i]); - - // tell BEAGLE to populate the transition matrices for the above edge lengths - beagleUpdateTransitionMatrices(instance, // instance - 0, // eigenIndex - probabilityIndicesEigenBuffer0, // probabilityIndices - NULL, // firstDerivativeIndices - NULL, // secondDerivativeIndices - edgeLengthsEigenBuffer0, // edgeLengths - listLengthEigenBuffer0); // count - - beagleUpdateTransitionMatrices(instance, // instance - 1, // eigenIndex - probabilityIndicesEigenBuffer1, // probabilityIndices - NULL, // firstDerivativeIndices - NULL, // secondDerivativeIndices - edgeLengthsEigenBuffer1, // edgeLengths - listLengthEigenBuffer1); // count - - int firstIndices[2] = { 4, 6 }; - int secondIndices[2] = { 5, 7 }; - int resultIndices[2] = { 0, 2 }; - - beagleConvolveTransitionMatrices(instance, // instance - firstIndices, // first indices - secondIndices, // second indices - resultIndices, // result indices - 2 // matrixCount - ); - - // for (int j = 0; j <= (6 + 1); j++) { - // printf("Matrix index %i: \n", j); - // printMatrix(j, stateCount, nRateCats, instance); - // } - - // create a list of partial likelihood update operations - // the order is [dest, destScaling, source1, matrix1, source2, matrix2] - BeagleOperation operations[2] = { - - { 3, // destination or parent partials buffer - BEAGLE_OP_NONE, // scaling buffer to write to - BEAGLE_OP_NONE, // scaling buffer to read from - 0, // first child partials buffer - 0, // transition matrix of first partials child buffer - 1, // second child partials buffer - 1 // transition matrix of second partials child buffer - }, - - { rootIndices[i], // destination or parent partials buffer - BEAGLE_OP_NONE, // scaling buffer to write to - BEAGLE_OP_NONE, // scaling buffer to read from - 2, // first child partials buffer - 2, // transition matrix of first partials child buffer - 3, // second child partials buffer - 3 // transition matrix of second partials child buffer - } - - }; - - // update the partials - beagleUpdatePartials(instance, // instance - operations, // eigenIndex - 2, // operationCount - cumulativeScalingIndices[i]); // cumulative scaling index - - }//END: nRootCount loop - - double *patternLogLik = (double*) malloc(sizeof(double) * nPatterns); - double logL = 0.0; - int returnCode = 0; - - // calculate the site likelihoods at the root node - returnCode = beagleCalculateRootLogLikelihoods(instance, // instance - (const int *) rootIndices, // bufferIndices - (const int *) categoryWeightsIndices, // weights - (const int *) stateFrequencyIndices, // stateFrequencies - cumulativeScalingIndices, // cumulative scaling index - nRootCount, // count - &logL); // outLogLikelihoods - - beagleGetSiteLogLikelihoods(instance, patternLogLik); - - double sumLogL = 0.0; - for (int i = 0; i < nPatterns; i++) { - sumLogL += patternLogLik[i] * patternWeights[i]; - } - - fprintf(stdout, "logL = %.5f \n", logL); - fprintf(stdout, "sumLogL = %.5f \n", sumLogL); - - free(weights); - free(patternWeights); - free(rootIndices); - free(categoryWeightsIndices); - free(stateFrequencyIndices); - free(cumulativeScalingIndices); - - free(patternLogLik); - - free(SimSeq1Partials); - free(SimSeq2Partials); - free(SimSeq3Partials); - - beagleFinalizeInstance(instance); - - return (EXIT_SUCCESS); -}//END: main - diff -Nru libhmsbeagle-2.1.2+20171110/.gitignore libhmsbeagle-2.1.2+git20180307/.gitignore --- libhmsbeagle-2.1.2+20171110/.gitignore 2011-06-16 19:31:42.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/.gitignore 1970-01-01 00:00:00.000000000 +0000 @@ -1,175 +0,0 @@ - -# / -/beagle-lib-1.0.pc -/configure -/Makefile.in -/config.log -/INSTALL -/COPYING -/Makefile -/.config -/config.status -/libtool -/autom4te.cache -/aclocal.m4 -/hmsbeagle-1.0.pc -/doc -/.idea -/Beagle-lib.iml -/hmsbeagle-1.pc - -# /examples/ -/examples/Makefile.in -/examples/Makefile -/examples/extensivetest - -# /examples/complextest/ -/examples/complextest/Makefile.in -/examples/complextest/Makefile -/examples/complextest/complextest -/examples/complextest/.deps - -# /examples/fourtaxon/ -/examples/fourtaxon/check_lnL_using_paup.nex -/examples/fourtaxon/fourtaxon.o -/examples/fourtaxon/fourtaxon -/examples/fourtaxon/Makefile.in -/examples/fourtaxon/.deps -/examples/fourtaxon/Makefile -/examples/fourtaxon/fourtaxonrun.sh - -# /examples/genomictest/ -/examples/genomictest/Makefile.in -/examples/genomictest/.deps -/examples/genomictest/Makefile -/examples/genomictest/genomictest -/examples/genomictest/genomictest.sh - -# /examples/matrixtest/ -/examples/matrixtest/Makefile.in -/examples/matrixtest/matrixtest -/examples/matrixtest/.deps -/examples/matrixtest/Makefile - -# /examples/oddstatetest/ -/examples/oddstatetest/Makefile.in -/examples/oddstatetest/.deps -/examples/oddstatetest/Makefile -/examples/oddstatetest/oddstatetest - -# /examples/tinytest/ -/examples/tinytest/Makefile.in -/examples/tinytest/.deps -/examples/tinytest/Makefile -/examples/tinytest/tinytest - -# /libhmsbeagle/ -/libhmsbeagle/config.h.in -/libhmsbeagle/Makefile.in -/libhmsbeagle/.deps -/libhmsbeagle/stamp-h1 -/libhmsbeagle/config.h -/libhmsbeagle/Makefile - -# /libhmsbeagle/CPU/ -/libhmsbeagle/CPU/Makefile.in -/libhmsbeagle/CPU/.deps -/libhmsbeagle/CPU/Makefile - -# /libhmsbeagle/GPU/ -/libhmsbeagle/GPU/Makefile.in -/libhmsbeagle/GPU/PeelingFunctions.linkinfo -/libhmsbeagle/GPU/.deps -/libhmsbeagle/GPU/TransitionFunctions.linkinfo -/libhmsbeagle/GPU/Makefile -/libhmsbeagle/GPU/BeagleCUDA_kernels.h -/libhmsbeagle/GPU/BeagleCUDA_kernels.ptx - -# /libhmsbeagle/GPU/kernels/ -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_64.ptx -/libhmsbeagle/GPU/kernels/Makefile.in -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_48.ptx -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels.h -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels.ptx -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_4.ptx -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_32.ptx -/libhmsbeagle/GPU/kernels/Makefile -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_xcode.h -/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_xcode.ptx - -# /libhmsbeagle/JNI/ -/libhmsbeagle/JNI/Makefile.in -/libhmsbeagle/JNI/.deps -/libhmsbeagle/JNI/Makefile - -# /libhmsbeagle/plugin/ -/libhmsbeagle/plugin/Makefile.in -/libhmsbeagle/plugin/.deps -/libhmsbeagle/plugin/Makefile - -# /m4/ -/m4/libtool.m4 -/m4/lt~obsolete.m4 -/m4/ltsugar.m4 -/m4/ltversion.m4 -/m4/ltoptions.m4 - -# /project/beagle-xcode/ -/project/beagle-xcode/build - -# /project/beagle-xcode/beagle-xcode.xcodeproj/ -/project/beagle-xcode/beagle-xcode.xcodeproj/*.pbxuser -/project/beagle-xcode/beagle-xcode.xcodeproj/*.perspectivev3 -/project/beagle-xcode/beagle-xcode.xcodeproj/xcuserdata -/project/beagle-xcode/beagle-xcode.xcodeproj/project.xcworkspace - -# other -.DS_Store -installed/ -libhmsbeagle/.libs/ -libhmsbeagle/CPU/.libs/ -libhmsbeagle/CPU/libhmsbeagle-cpu-sse.la -libhmsbeagle/CPU/libhmsbeagle-cpu.la -libhmsbeagle/CPU/libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -libhmsbeagle/CPU/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo -libhmsbeagle/GPU/.libs/ -libhmsbeagle/GPU/libhmsbeagle-cuda.la -libhmsbeagle/GPU/libhmsbeagle_cuda_la-CUDAPlugin.lo -libhmsbeagle/GPU/libhmsbeagle_cuda_la-GPUImplHelper.lo -libhmsbeagle/GPU/libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo -libhmsbeagle/GPU/libhmsbeagle_cuda_la-KernelLauncher.lo -libhmsbeagle/GPU/libhmsbeagle_cuda_la-KernelResource.lo -libhmsbeagle/libhmsbeagle-jni.la -libhmsbeagle/libhmsbeagle.la -libhmsbeagle/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -libhmsbeagle/libhmsbeagle_la-beagle.lo -libhmsbeagle/plugin/.libs/ -libhmsbeagle/plugin/libplugin.la -libhmsbeagle/plugin/libplugin_la-Plugin.lo -libhmsbeagle/plugin/libplugin_la-UnixSharedLibrary.lo -project/.DS_Store -project/beagle-xcode/.DS_Store -project/beagle-xcode/BEAGLEv1.0.pkg -examples/complextest/.libs/ -examples/complextest/complextest.o -examples/fourtaxon/.libs/ -examples/genomictest/.libs/ -examples/genomictest/genomictest.o -examples/genomictest/linalg.o -examples/matrixtest/.libs/ -examples/matrixtest/matrixtest.o -examples/oddstatetest/.libs/ -examples/oddstatetest/oddstatetest.o -examples/tinytest/.libs/ -examples/tinytest/tinytest.o -libhmsbeagle/GPU/kernels/BeagleOpenCL_kernels.h -libhmsbeagle/GPU/kernels/BeagleOpenCL_kernels_xcode.h -libhmsbeagle/GPU/libhmsbeagle-opencl.la -libhmsbeagle/GPU/libhmsbeagle_opencl_la-GPUImplHelper.lo -libhmsbeagle/GPU/libhmsbeagle_opencl_la-GPUInterfaceOpenCL.lo -libhmsbeagle/GPU/libhmsbeagle_opencl_la-KernelLauncher.lo -libhmsbeagle/GPU/libhmsbeagle_opencl_la-KernelResource.lo -libhmsbeagle/GPU/libhmsbeagle_opencl_la-OpenCLPlugin.lo -libhmsbeagle/config.h.in~ -project/beagle-xcode/BEAGLE-1.0.pkg - diff -Nru libhmsbeagle-2.1.2+20171110/libhmsbeagle/GPU/kernels/kernels4.cu libhmsbeagle-2.1.2+git20180307/libhmsbeagle/GPU/kernels/kernels4.cu --- libhmsbeagle-2.1.2+20171110/libhmsbeagle/GPU/kernels/kernels4.cu 2014-03-06 12:16:25.000000000 +0000 +++ libhmsbeagle-2.1.2+git20180307/libhmsbeagle/GPU/kernels/kernels4.cu 2018-03-07 14:18:17.000000000 +0000 @@ -321,13 +321,13 @@ int patIdx16pat4 = multBy16(patIdx) | (tx & 0xC);\ sum1 = sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i];\ sum2 = sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i];\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2); @@ -339,11 +339,11 @@ int i = pat;\ int patIdx16pat4 = multBy16(patIdx) | (tx & 0xC);\ sum2 = sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i];\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix2[multBy4(i) | state], sPartials2[patIdx16pat4 | i], sum2); #define SUM_PARTIALS_SINGLE_4_GPU()\ @@ -351,11 +351,11 @@ int i = pat;\ int patIdx16pat4 = multBy16(patIdx) | (tx & 0xC);\ sum1 = sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i];\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA( sMatrix1[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1); #define SUM_STATES_SINGLE_4_GPU()\ @@ -373,15 +373,15 @@ sum1 = sMatrix1[ multBy4(i) | state] * sPartials1[patIdx16pat4 | i];\ sumFirstDeriv = sMatrixFirstDeriv[ multBy4(i) | state] * sPartials1[patIdx16pat4 | i];\ sumSecondDeriv = sMatrixSecondDeriv[multBy4(i) | state] * sPartials1[patIdx16pat4 | i];\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA(sMatrix1[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA(sMatrixFirstDeriv[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumFirstDeriv);\ FMA(sMatrixSecondDeriv[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumSecondDeriv);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA(sMatrix1[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA(sMatrixFirstDeriv[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumFirstDeriv);\ FMA(sMatrixSecondDeriv[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumSecondDeriv);\ - i = (++i) & 0x3;\ + i = (i + 1) & 0x3;\ FMA(sMatrix1[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sum1);\ FMA(sMatrixFirstDeriv[ multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumFirstDeriv);\ FMA(sMatrixSecondDeriv[multBy4(i) | state], sPartials1[patIdx16pat4 | i], sumSecondDeriv); @@ -1194,15 +1194,15 @@ sum1 = sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 = sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; @@ -1283,15 +1283,15 @@ sum1 = sMatrix1[i * 4 + state] * sPartials1[patIdx * 16 + pat * 4 + i]; sum2 = sMatrix2[i * 4 + state] * sPartials2[patIdx * 16 + pat * 4 + i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[i * 4 + state] * sPartials1[patIdx * 16 + pat * 4 + i]; sum2 += sMatrix2[i * 4 + state] * sPartials2[patIdx * 16 + pat * 4 + i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[i * 4 + state] * sPartials1[patIdx * 16 + pat * 4 + i]; sum2 += sMatrix2[i * 4 + state] * sPartials2[patIdx * 16 + pat * 4 + i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[i * 4 + state] * sPartials1[patIdx * 16 + pat * 4 + i]; sum2 += sMatrix2[i * 4 + state] * sPartials2[patIdx * 16 + pat * 4 + i]; @@ -1358,15 +1358,15 @@ sum1 = sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 = sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i]; - i = (++i) & 0x3; + i = (i + 1) & 0x3; sum1 += sMatrix1[multBy4(i) | state] * sPartials1[patIdx16pat4 | i]; sum2 += sMatrix2[multBy4(i) | state] * sPartials2[patIdx16pat4 | i];