[med-svn] [crac] branch master updated (5e8992b -> 3c80cc2)
Andreas Tille
tille at debian.org
Sat Sep 10 21:54:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository crac.
from 5e8992b Add install files to install into right packages
new afb1587 Fix watch file, bump version
new 5db35e9 New upstream version 2.5.0
new 3d496c5 Merge tag 'upstream/2.5.0'
new 61b4459 cme fix dpkg-control
new 328a4a3 Add new Build-Depends: libhts-dev
new 3c80cc2 New publication
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +-
debian/changelog | 4 +-
debian/control | 22 +-
debian/upstream/metadata | 33 +-
debian/watch | 2 +-
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 +
.../config => libJellyfish-2.0}/config.guess | 346 +-
src/libJellyfish-2.0/config.h.in | 89 +
.../config => libJellyfish-2.0}/config.sub | 115 +-
.../configure | 6960 +++----
src/libJellyfish-2.0/configure.ac | 100 +
.../depcomp | 531 +-
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 +
.../config => libJellyfish-2.0}/install-sh | 35 +-
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 +-
src/{libgzstream => libReadsReader}/Makefile.am | 13 +-
src/{ => libReadsReader}/Makefile.in | 547 +-
.../src => libReadsReader}/kseq/Makefile.am | 0
.../src => libReadsReader}/kseq/Makefile.in | 224 +-
.../src => libReadsReader}/kseq/kseq.h | 0
src/libReadsReader/readsReader.cpp | 361 +
.../src => libReadsReader}/readsReader.h | 189 +-
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/{bug => 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 +
328 files changed, 100528 insertions(+), 65446 deletions(-)
create mode 100755 config/compile
mode change 100755 => 100644 config/ltmain.sh
copy aclocal.m4 => config/m4/libtool.m4 (71%)
create mode 100644 config/m4/ltoptions.m4
create mode 100644 config/m4/ltsugar.m4
create mode 100644 config/m4/ltversion.m4
create mode 100644 config/m4/lt~obsolete.m4
create mode 100755 config/test-driver
delete mode 100644 doc/CeCILL.texi
delete mode 100644 doc/Makefile.am
delete mode 100644 doc/Makefile.in
delete mode 100644 doc/crac.info
delete mode 100644 doc/crac.texi
delete mode 100644 doc/package.texi.in
create mode 100644 src/Bitset.cpp
create mode 100644 src/Bitset.h
create mode 100644 src/BreakList.cpp
create mode 100644 src/BreakList.h
create mode 100644 src/GkReadIndex.cpp
create mode 100644 src/GkReadIndex.h
create mode 100644 src/JellyReadIndex.cpp
create mode 100644 src/JellyReadIndex.h
create mode 100644 src/Read.h
create mode 100644 src/ReadIndex.h
create mode 100755 src/libGkArrays/config/compile
copy aclocal.m4 => src/libGkArrays/config/m4/libtool.m4 (72%)
create mode 100644 src/libGkArrays/config/m4/ltoptions.m4
create mode 100644 src/libGkArrays/config/m4/ltsugar.m4
create mode 100644 src/libGkArrays/config/m4/ltversion.m4
create mode 100644 src/libGkArrays/config/m4/lt~obsolete.m4
create mode 100755 src/libGkArrays/config/test-driver
create mode 100755 src/libGkArrays/src/libProgressBar-1.2.0/compile
mode change 100755 => 100644 src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh
copy aclocal.m4 => src/libGkArrays/src/libProgressBar-1.2.0/m4/libtool.m4 (72%)
create mode 100644 src/libGkArrays/src/libProgressBar-1.2.0/m4/ltoptions.m4
create mode 100644 src/libGkArrays/src/libProgressBar-1.2.0/m4/ltsugar.m4
create mode 100644 src/libGkArrays/src/libProgressBar-1.2.0/m4/ltversion.m4
create mode 100644 src/libGkArrays/src/libProgressBar-1.2.0/m4/lt~obsolete.m4
create mode 100644 src/libJellyfish-2.0/HalfLICENSE
create mode 100644 src/libJellyfish-2.0/LICENSE
create mode 100644 src/libJellyfish-2.0/Makefile.am
create mode 100644 src/libJellyfish-2.0/Makefile.in
create mode 100644 src/libJellyfish-2.0/README
create mode 100644 src/libJellyfish-2.0/aclocal.m4
create mode 100755 src/libJellyfish-2.0/compile
copy src/{libGkArrays/config => libJellyfish-2.0}/config.guess (86%)
create mode 100644 src/libJellyfish-2.0/config.h.in
copy src/{libGkArrays/config => libJellyfish-2.0}/config.sub (93%)
copy src/{libGkArrays/src/libProgressBar-1.2.0 => libJellyfish-2.0}/configure (79%)
create mode 100644 src/libJellyfish-2.0/configure.ac
copy src/{libGkArrays/src/libProgressBar-1.2.0 => libJellyfish-2.0}/depcomp (50%)
create mode 100644 src/libJellyfish-2.0/doc/jellyfish.man
create mode 100644 src/libJellyfish-2.0/doc/jellyfish.pdf
create mode 100755 src/libJellyfish-2.0/gtest.mk
create mode 100644 src/libJellyfish-2.0/include/jellyfish/allocators_mmap.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_bits_array.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_field.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_gcc.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/backtrace.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/binary_dumper.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_common.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_counter2.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_filter.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/circular_buffer.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/compare_and_swap.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/cooperative_pool.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/cooperative_pool2.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/cpp_array.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/divisor.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/dumper.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/err.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/file_header.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/generator_manager.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/generic_file_header.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/hash_counter.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/int128.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/jellyfish.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/json.h
create mode 100644 src/libJellyfish-2.0/include/jellyfish/large_hash_array.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/large_hash_iterator.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/locks_pthread.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mapped_file.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_dna.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_dna_bloom_counter.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_heap.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_iterator.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_overlap_sequence_parser.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_qual_iterator.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/misc.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/offsets_key_value.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/rectangular_binary_matrix.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/simple_circular_buffer.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/sorted_dumper.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/stdio_filebuf.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/storage.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/stream_iterator.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/stream_manager.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/text_dumper.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/thread_exec.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/time.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/token_ring.hpp
create mode 100644 src/libJellyfish-2.0/include/jellyfish/whole_sequence_parser.hpp
copy src/{libGkArrays/config => libJellyfish-2.0}/install-sh (94%)
create mode 100644 src/libJellyfish-2.0/jellyfish-2.0.pc.in
create mode 100644 src/libJellyfish-2.0/jellyfish/dbg.hpp
create mode 100644 src/libJellyfish-2.0/jellyfish/fstream_default.hpp
create mode 100644 src/libJellyfish-2.0/jellyfish/merge_files.hpp
create mode 100644 src/libJellyfish-2.0/jellyfish/randomc.h
create mode 100644 src/libJellyfish-2.0/lib/allocators_mmap.cc
create mode 100644 src/libJellyfish-2.0/lib/err.cc
create mode 100644 src/libJellyfish-2.0/lib/generator_manager.cc
create mode 100644 src/libJellyfish-2.0/lib/int128.cc
create mode 100644 src/libJellyfish-2.0/lib/jsoncpp.cpp
create mode 100644 src/libJellyfish-2.0/lib/mer_dna.cc
create mode 100644 src/libJellyfish-2.0/lib/misc.cc
create mode 100644 src/libJellyfish-2.0/lib/rectangular_binary_matrix.cc
create mode 100644 src/libJellyfish-2.0/lib/storage.cc
create mode 100644 src/libJellyfish-2.0/lib/thread_exec.cc
create mode 100644 src/libJellyfish-2.0/lib/time.cc
copy src/{libGkArrays/src/libProgressBar-1.2.0 => libJellyfish-2.0}/ltmain.sh (67%)
mode change 100755 => 100644
copy aclocal.m4 => src/libJellyfish-2.0/m4/libtool.m4 (71%)
create mode 100644 src/libJellyfish-2.0/m4/ltoptions.m4
create mode 100644 src/libJellyfish-2.0/m4/ltsugar.m4
create mode 100644 src/libJellyfish-2.0/m4/ltversion.m4
create mode 100644 src/libJellyfish-2.0/m4/lt~obsolete.m4
create mode 100755 src/libJellyfish-2.0/missing
create mode 100644 src/libJellyfish-2.0/unit_tests/gtest/gtest.h
create mode 100644 src/libJellyfish-2.0/unit_tests/gtest/src/gtest-all.cc
create mode 100644 src/libJellyfish-2.0/unit_tests/gtest/src/gtest_main.cc
create mode 100644 src/libReadsInfo/bamUtils.cpp
create mode 100644 src/libReadsInfo/bamUtils.h
create mode 100644 src/libReadsInfo/samHeader.cpp
create mode 100644 src/libReadsInfo/samHeader.h
copy src/{libgzstream => libReadsReader}/Makefile.am (96%)
copy src/{ => libReadsReader}/Makefile.in (62%)
copy src/{libGkArrays/src => libReadsReader}/kseq/Makefile.am (100%)
copy src/{libGkArrays/src => libReadsReader}/kseq/Makefile.in (77%)
copy src/{libGkArrays/src => libReadsReader}/kseq/kseq.h (100%)
create mode 100644 src/libReadsReader/readsReader.cpp
copy src/{libGkArrays/src => libReadsReader}/readsReader.h (54%)
create mode 100644 test_f/bug/bug-14958-genome.fa
create mode 100644 test_f/bug/bug-14958-read.fa
create mode 100644 test_f/bug/bug-14958.should_get
create mode 100644 test_f/bug/bug-16502-genome.fa
create mode 100644 test_f/bug/bug-16502-read.fa
create mode 100644 test_f/bug/bug-16502.should_get
create mode 100644 test_f/bug/bug-17749-genome.fa
create mode 100644 test_f/bug/bug-17749-read.fa
create mode 100644 test_f/bug/bug-17749.should_get
create mode 100644 test_f/bug/bug-18180-genome.fa
create mode 100644 test_f/bug/bug-18180-read.fa
create mode 100644 test_f/bug/bug-18180.should_get
create mode 100644 test_f/bug/bug-18409-genome.fa
create mode 100644 test_f/bug/bug-18409-read.fa
create mode 100644 test_f/bug/bug-18409.should_get
create mode 100644 test_f/bug/bug-18435-genome.fa
create mode 100644 test_f/bug/bug-18435-read.fa
create mode 100644 test_f/bug/bug-18435.should_get
create mode 100644 test_f/bug/bug-18522-genome.fa
create mode 100644 test_f/bug/bug-18522-read.fa
create mode 100644 test_f/bug/bug-18522.should_get
create mode 100644 test_f/bug/bug-18524-genome.fa
create mode 100644 test_f/bug/bug-18524-read.fa
create mode 100644 test_f/bug/bug-18524.should_get
create mode 100644 test_f/bug/bug-18568-genome.fa
create mode 100644 test_f/bug/bug-18568-read.fa
create mode 100644 test_f/bug/bug-18568.should_get
create mode 100644 test_f/bug/bug-18793-genome.fa
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create mode 100644 test_f/bug/bug-18793.should_get
create mode 100644 test_f/bug/bug-2015-12-08-genome.fa
create mode 100644 test_f/bug/bug-2015-12-08-read1.fa
create mode 100644 test_f/bug/bug-2015-12-08-read2.fa
create mode 100644 test_f/bug/bug-2015-12-08.should_get
create mode 100644 test_f/bug/bug-case-sensitive-genome.fa
create mode 100644 test_f/bug/bug-case-sensitive-read.fa
create mode 100644 test_f/bug/bug-case-sensitive.should_get
create mode 100644 test_f/causes/biotag.fa
create mode 100644 test_f/causes/biotag.fa.should_get
copy test_f/{causes => splices_adjust}/Makefile.am (100%)
copy test_f/{bug => splices_adjust}/Makefile.in (81%)
create mode 100644 test_f/splices_adjust/genome.fa
create mode 100644 test_f/splices_adjust/splice.fa
create mode 100644 test_f/splices_adjust/splice.should_get
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