[med-svn] [crac] 03/06: Merge tag 'upstream/2.5.0'
Andreas Tille
tille at debian.org
Sat Sep 10 21:54:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crac.
commit 3d496c50ae21e25518cd84d8acc013abe2f50ebd
Merge: afb1587 5db35e9
Author: Andreas Tille <tille at debian.org>
Date: Sat Sep 10 23:42:10 2016 +0200
Merge tag 'upstream/2.5.0'
Upstream version 2.5.0
COPYING | 1547 +-
ChangeLog | 437 +-
Makefile.am | 3 -
Makefile.in | 419 +-
README | 106 +-
aclocal.m4 | 8687 +-------
config/compile | 347 +
config/config.h.in | 9 +
config/ltmain.sh | 4016 ++--
aclocal.m4 => config/m4/libtool.m4 | 3862 ++--
config/m4/ltoptions.m4 | 384 +
config/m4/ltsugar.m4 | 123 +
config/m4/ltversion.m4 | 23 +
config/m4/lt~obsolete.m4 | 98 +
config/test-driver | 139 +
configure | 6074 +++---
configure.ac | 338 +-
doc/CeCILL.texi | 571 -
doc/Makefile.am | 131 -
doc/Makefile.in | 767 -
doc/crac.info | 806 -
doc/crac.texi | 218 -
doc/package.texi.in | 2 -
man/Makefile.in | 169 +-
man/crac.1.in | 192 +-
scripts/Makefile.in | 146 +-
scripts/crac-client | 2 +-
src/Bitset.cpp | 71 +
src/Bitset.h | 69 +
src/BreakList.cpp | 133 +
src/BreakList.h | 117 +
src/CandidatBreak.cpp | 124 +-
src/CandidatBreak.h | 112 +-
src/Classifier.cpp | 892 +-
src/Classifier.h | 263 +-
src/GkReadIndex.cpp | 69 +
src/GkReadIndex.h | 103 +
src/JellyReadIndex.cpp | 102 +
src/JellyReadIndex.h | 158 +
src/Makefile.am | 42 +-
src/Makefile.in | 443 +-
src/Parameters.cpp | 142 +-
src/Parameters.h | 142 +-
src/Read.h | 133 +
src/ReadIndex.h | 92 +
src/Support.cpp | 1206 +-
src/Support.h | 325 +-
src/SupportBreak.cpp | 445 +-
src/SupportBreak.h | 222 +-
src/basic.h | 114 +-
src/classifyTags.cpp | 357 +-
src/classifyTags.h | 165 +-
src/const.h | 142 +-
src/crac.cpp | 561 +-
src/libGkArrays/Makefile.in | 417 +-
src/libGkArrays/aclocal.m4 | 8687 +-------
src/libGkArrays/config/compile | 347 +
src/libGkArrays/config/ltmain.sh | 4016 ++--
aclocal.m4 => src/libGkArrays/config/m4/libtool.m4 | 3564 ++--
src/libGkArrays/config/m4/ltoptions.m4 | 369 +
src/libGkArrays/config/m4/ltsugar.m4 | 123 +
src/libGkArrays/config/m4/ltversion.m4 | 23 +
src/libGkArrays/config/m4/lt~obsolete.m4 | 98 +
src/libGkArrays/config/test-driver | 139 +
src/libGkArrays/configure | 4994 +++--
src/libGkArrays/configure.ac | 7 +-
src/libGkArrays/doc/Makefile.in | 277 +-
src/libGkArrays/doc/libGkArrays.info | 285 +-
src/libGkArrays/src/Makefile.in | 430 +-
src/libGkArrays/src/gkArrays.cpp | 1 +
src/libGkArrays/src/gkSABuilder.cpp | 1 +
src/libGkArrays/src/kseq/Makefile.in | 210 +-
.../src/libProgressBar-1.2.0/Makefile.in | 421 +-
.../src/libProgressBar-1.2.0/aclocal.m4 | 8687 +-------
src/libGkArrays/src/libProgressBar-1.2.0/compile | 347 +
src/libGkArrays/src/libProgressBar-1.2.0/configure | 4824 +++--
.../src/libProgressBar-1.2.0/doc/Makefile.am | 2 +-
.../src/libProgressBar-1.2.0/doc/Makefile.in | 279 +-
.../src/libProgressBar-1.2.0/doc/libProgressBar.3 | 2 +-
.../libProgressBar/Makefile.in | 333 +-
.../libProgressBar/config.h.in | 3 +
src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh | 4016 ++--
.../src/libProgressBar-1.2.0/m4/libtool.m4 | 3564 ++--
.../src/libProgressBar-1.2.0/m4/ltoptions.m4 | 369 +
.../src/libProgressBar-1.2.0/m4/ltsugar.m4 | 123 +
.../src/libProgressBar-1.2.0/m4/ltversion.m4 | 23 +
.../src/libProgressBar-1.2.0/m4/lt~obsolete.m4 | 98 +
src/libGkArrays/src/sux/Makefile.in | 210 +-
src/libGkArrays/tests/Makefile.in | 743 +-
src/libJellyfish-2.0/HalfLICENSE | 34 +
src/libJellyfish-2.0/LICENSE | 674 +
src/libJellyfish-2.0/Makefile.am | 206 +
src/libJellyfish-2.0/Makefile.in | 1410 ++
src/libJellyfish-2.0/README | 98 +
src/libJellyfish-2.0/aclocal.m4 | 1369 ++
src/libJellyfish-2.0/compile | 347 +
src/libJellyfish-2.0/config.guess | 1420 ++
src/libJellyfish-2.0/config.h.in | 89 +
src/libJellyfish-2.0/config.sub | 1794 ++
.../configure | 6960 +++----
src/libJellyfish-2.0/configure.ac | 100 +
src/libJellyfish-2.0/depcomp | 791 +
src/libJellyfish-2.0/doc/jellyfish.man | 647 +
src/libJellyfish-2.0/doc/jellyfish.pdf | Bin 0 -> 242134 bytes
src/libJellyfish-2.0/gtest.mk | 18 +
.../include/jellyfish/allocators_mmap.hpp | 78 +
.../include/jellyfish/atomic_bits_array.hpp | 196 +
.../include/jellyfish/atomic_field.hpp | 157 +
.../include/jellyfish/atomic_gcc.hpp | 68 +
.../include/jellyfish/backtrace.hpp | 18 +
.../include/jellyfish/binary_dumper.hpp | 224 +
.../include/jellyfish/bloom_common.hpp | 129 +
.../include/jellyfish/bloom_counter2.hpp | 221 +
.../include/jellyfish/bloom_filter.hpp | 164 +
.../include/jellyfish/circular_buffer.hpp | 200 +
.../include/jellyfish/compare_and_swap.hpp | 80 +
.../include/jellyfish/cooperative_pool.hpp | 258 +
.../include/jellyfish/cooperative_pool2.hpp | 283 +
.../include/jellyfish/cpp_array.hpp | 156 +
src/libJellyfish-2.0/include/jellyfish/divisor.hpp | 150 +
src/libJellyfish-2.0/include/jellyfish/dumper.hpp | 103 +
src/libJellyfish-2.0/include/jellyfish/err.hpp | 133 +
.../include/jellyfish/file_header.hpp | 112 +
.../include/jellyfish/generator_manager.hpp | 163 +
.../include/jellyfish/generic_file_header.hpp | 255 +
.../include/jellyfish/hash_counter.hpp | 244 +
src/libJellyfish-2.0/include/jellyfish/int128.hpp | 203 +
.../include/jellyfish/jellyfish.hpp | 42 +
src/libJellyfish-2.0/include/jellyfish/json.h | 1855 ++
.../include/jellyfish/large_hash_array.hpp | 994 +
.../include/jellyfish/large_hash_iterator.hpp | 260 +
.../include/jellyfish/locks_pthread.hpp | 211 +
.../include/jellyfish/mapped_file.hpp | 220 +
src/libJellyfish-2.0/include/jellyfish/mer_dna.hpp | 729 +
.../include/jellyfish/mer_dna_bloom_counter.hpp | 50 +
.../include/jellyfish/mer_heap.hpp | 115 +
.../include/jellyfish/mer_iterator.hpp | 100 +
.../jellyfish/mer_overlap_sequence_parser.hpp | 279 +
.../include/jellyfish/mer_qual_iterator.hpp | 118 +
src/libJellyfish-2.0/include/jellyfish/misc.hpp | 247 +
.../include/jellyfish/offsets_key_value.hpp | 277 +
.../jellyfish/rectangular_binary_matrix.hpp | 379 +
.../include/jellyfish/simple_circular_buffer.hpp | 134 +
.../include/jellyfish/sorted_dumper.hpp | 115 +
.../include/jellyfish/stdio_filebuf.hpp | 170 +
src/libJellyfish-2.0/include/jellyfish/storage.hpp | 37 +
.../include/jellyfish/stream_iterator.hpp | 90 +
.../include/jellyfish/stream_manager.hpp | 158 +
.../include/jellyfish/text_dumper.hpp | 88 +
.../include/jellyfish/thread_exec.hpp | 53 +
src/libJellyfish-2.0/include/jellyfish/time.hpp | 92 +
.../include/jellyfish/token_ring.hpp | 87 +
.../include/jellyfish/whole_sequence_parser.hpp | 150 +
src/libJellyfish-2.0/install-sh | 527 +
src/libJellyfish-2.0/jellyfish-2.0.pc.in | 10 +
src/libJellyfish-2.0/jellyfish/dbg.hpp | 153 +
src/libJellyfish-2.0/jellyfish/fstream_default.hpp | 68 +
src/libJellyfish-2.0/jellyfish/merge_files.hpp | 30 +
src/libJellyfish-2.0/jellyfish/randomc.h | 198 +
src/libJellyfish-2.0/lib/allocators_mmap.cc | 114 +
src/libJellyfish-2.0/lib/err.cc | 31 +
src/libJellyfish-2.0/lib/generator_manager.cc | 282 +
src/libJellyfish-2.0/lib/int128.cc | 94 +
src/libJellyfish-2.0/lib/jsoncpp.cpp | 4230 ++++
src/libJellyfish-2.0/lib/mer_dna.cc | 23 +
src/libJellyfish-2.0/lib/misc.cc | 102 +
.../lib/rectangular_binary_matrix.cc | 216 +
src/libJellyfish-2.0/lib/storage.cc | 51 +
src/libJellyfish-2.0/lib/thread_exec.cc | 44 +
src/libJellyfish-2.0/lib/time.cc | 19 +
.../ltmain.sh | 4016 ++--
aclocal.m4 => src/libJellyfish-2.0/m4/libtool.m4 | 3862 ++--
src/libJellyfish-2.0/m4/ltoptions.m4 | 384 +
src/libJellyfish-2.0/m4/ltsugar.m4 | 123 +
src/libJellyfish-2.0/m4/ltversion.m4 | 23 +
src/libJellyfish-2.0/m4/lt~obsolete.m4 | 98 +
src/libJellyfish-2.0/missing | 215 +
src/libJellyfish-2.0/unit_tests/gtest/gtest.h | 20061 +++++++++++++++++++
.../unit_tests/gtest/src/gtest-all.cc | 9592 +++++++++
.../unit_tests/gtest/src/gtest_main.cc | 38 +
src/libReadsInfo/BioTagIndelInfo.cpp | 114 +-
src/libReadsInfo/BioTagIndelInfo.h | 114 +-
src/libReadsInfo/BioUndeterminedInfo.cpp | 120 +-
src/libReadsInfo/BioUndeterminedInfo.h | 135 +-
src/libReadsInfo/Cigar.cpp | 138 +-
src/libReadsInfo/Cigar.h | 135 +-
src/libReadsInfo/DuplicationInfo.cpp | 114 +-
src/libReadsInfo/DuplicationInfo.h | 114 +-
src/libReadsInfo/IndelInfo.cpp | 114 +-
src/libReadsInfo/IndelInfo.h | 114 +-
src/libReadsInfo/Makefile.am | 2 +
src/libReadsInfo/Makefile.in | 601 +-
src/libReadsInfo/SNPInfo.cpp | 114 +-
src/libReadsInfo/SNPInfo.h | 114 +-
src/libReadsInfo/SeqErrInfo.cpp | 114 +-
src/libReadsInfo/SeqErrInfo.h | 114 +-
src/libReadsInfo/SpliceInfo.cpp | 114 +-
src/libReadsInfo/SpliceInfo.h | 114 +-
src/libReadsInfo/SpliceInterInfo.cpp | 155 +-
src/libReadsInfo/SpliceInterInfo.h | 122 +-
src/libReadsInfo/SpliceIntraInfo.cpp | 114 +-
src/libReadsInfo/SpliceIntraInfo.h | 114 +-
src/libReadsInfo/SpliceNoCoverInfo.cpp | 114 +-
src/libReadsInfo/SpliceNoCoverInfo.h | 114 +-
src/libReadsInfo/SplicingInfo.cpp | 114 +-
src/libReadsInfo/SplicingInfo.h | 114 +-
src/libReadsInfo/bamUtils.cpp | 101 +
src/libReadsInfo/bamUtils.h | 55 +
src/libReadsInfo/cigarTypes.cpp | 114 +-
src/libReadsInfo/cigarTypes.h | 114 +-
src/libReadsInfo/genericInfo.cpp | 114 +-
src/libReadsInfo/genericInfo.h | 114 +-
src/libReadsInfo/repetitionInfo.cpp | 114 +-
src/libReadsInfo/repetitionInfo.h | 114 +-
src/libReadsInfo/samHeader.cpp | 162 +
src/libReadsInfo/samHeader.h | 128 +
src/libReadsInfo/samLine.cpp | 457 +-
src/libReadsInfo/samLine.h | 247 +-
src/libReadsInfo/tagInfo.cpp | 655 +-
src/libReadsInfo/tagInfo.h | 149 +-
src/libReadsInfo/undeterminedErrorInfo.cpp | 119 +-
src/libReadsInfo/undeterminedErrorInfo.h | 125 +-
{test_f/bug => src/libReadsReader}/Makefile.am | 16 +-
src/{ => libReadsReader}/Makefile.in | 547 +-
.../bug => src/libReadsReader/kseq}/Makefile.am | 39 +-
.../src => libReadsReader}/kseq/Makefile.in | 224 +-
src/libReadsReader/kseq/kseq.h | 229 +
src/libReadsReader/readsReader.cpp | 361 +
src/libReadsReader/readsReader.h | 379 +
src/libSSA/GenomeInfo.cpp | 152 +-
src/libSSA/GenomeInfo.h | 139 +-
src/libSSA/HuffAlphabetRank.cpp | 112 +-
src/libSSA/HuffAlphabetRank.h | 114 +-
src/libSSA/Huffman_Codes.cpp | 114 +-
src/libSSA/Huffman_Codes.h | 114 +-
src/libSSA/Makefile.in | 298 +-
src/libSSA/SSA.cpp | 112 +-
src/libSSA/SSA.h | 114 +-
src/libSSA/basic.h | 114 +-
src/libSSA/bitarray.cpp | 112 +-
src/libSSA/bitarray.h | 114 +-
src/libSSA/bitrankw32int.cpp | 176 +-
src/libSSA/bitrankw32int.h | 122 +-
src/libSSA/chrPosition.cpp | 125 +-
src/libSSA/chrPosition.h | 127 +-
src/libSSA/cracIndex.cpp | 132 +-
src/libSSA/cracIndex.h | 120 +-
src/libSSA/locateOnGenome.cpp | 121 +-
src/libSSA/locateOnGenome.h | 114 +-
src/libSSA/locateTags.cpp | 326 +-
src/libSSA/locateTags.h | 129 +-
src/libSSA/utils.cpp | 114 +-
src/libSSA/utils.h | 114 +-
src/libgzstream/Makefile.in | 280 +-
src/locateServer.cpp | 395 +-
src/locateServer.h | 115 +-
src/types.h | 116 +-
src/utils.cpp | 151 +-
src/utils.h | 125 +-
test_f/Makefile.am | 9 +-
test_f/Makefile.in | 780 +-
test_f/bug/Makefile.am | 2 +-
test_f/bug/Makefile.in | 129 +-
test_f/bug/bug-14958-genome.fa | 4 +
test_f/bug/bug-14958-read.fa | 1 +
test_f/bug/bug-14958.should_get | 6 +
test_f/bug/bug-15672.should_get | 4 +-
test_f/bug/bug-15847.should_get | 4 +-
test_f/bug/bug-16403-genome.fa | 2 +-
test_f/bug/bug-16403.should_get | 2 +-
test_f/bug/bug-16502-genome.fa | 12 +
test_f/bug/bug-16502-read.fa | 1 +
test_f/bug/bug-16502.should_get | 6 +
test_f/bug/bug-16931.should_get | 2 +-
test_f/bug/bug-17175.should_get | 2 +-
test_f/bug/bug-17749-genome.fa | 8 +
test_f/bug/bug-17749-read.fa | 8 +
test_f/bug/bug-17749.should_get | 9 +
test_f/bug/bug-18180-genome.fa | 2 +
test_f/bug/bug-18180-read.fa | 2 +
test_f/bug/bug-18180.should_get | 6 +
test_f/bug/bug-18409-genome.fa | 2 +
test_f/bug/bug-18409-read.fa | 6 +
test_f/bug/bug-18409.should_get | 5 +
test_f/bug/bug-18435-genome.fa | 4 +
test_f/bug/bug-18435-read.fa | 2 +
test_f/bug/bug-18435.should_get | 6 +
test_f/bug/bug-18522-genome.fa | 4 +
test_f/bug/bug-18522-read.fa | 4 +
test_f/bug/bug-18522.should_get | 6 +
test_f/bug/bug-18524-genome.fa | 2 +
test_f/bug/bug-18524-read.fa | 4 +
test_f/bug/bug-18524.should_get | 6 +
test_f/bug/bug-18568-genome.fa | 2 +
test_f/bug/bug-18568-read.fa | 2 +
test_f/bug/bug-18568.should_get | 6 +
test_f/bug/bug-18793-genome.fa | 2 +
test_f/bug/bug-18793-read.fa | 6 +
test_f/bug/bug-18793.should_get | 8 +
test_f/bug/bug-2015-12-08-genome.fa | 4 +
test_f/bug/bug-2015-12-08-read1.fa | 2 +
test_f/bug/bug-2015-12-08-read2.fa | 2 +
test_f/bug/bug-2015-12-08.should_get | 9 +
test_f/bug/bug-case-sensitive-genome.fa | 2 +
test_f/bug/bug-case-sensitive-read.fa | 25 +
test_f/bug/bug-case-sensitive.should_get | 18 +
test_f/causes/Makefile.am | 2 +-
test_f/causes/Makefile.in | 129 +-
test_f/causes/biotag.fa | 16 +
test_f/causes/biotag.fa.should_get | 15 +
test_f/causes/snp.fa.should_get | 6 +-
test_f/cigar/Makefile.am | 2 +-
test_f/cigar/Makefile.in | 129 +-
test_f/cigar/consistency.should_get | 10 +-
test_f/cigar/consistency3.should_get | 12 +-
test_f/cigar/genome.fasta | 2 +-
test_f/cigar/reads_sam1.fasta | 2 +-
test_f/cigar/reads_sam2.fasta | 4 +-
test_f/should-get.sh | 7 +-
test_f/{causes => splices_adjust}/Makefile.am | 0
test_f/{cigar => splices_adjust}/Makefile.in | 135 +-
test_f/splices_adjust/genome.fa | 4 +
test_f/splices_adjust/splice.fa | 8 +
test_f/splices_adjust/splice.should_get | 10 +
324 files changed, 105036 insertions(+), 64843 deletions(-)
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