[med-svn] [axe-demultiplexer] 02/06: Merge tag 'upstream/0.3.2+dfsg'
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Dec 1 01:52:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository axe-demultiplexer.
commit 5e8a9e72d77ae0a19d5c55b36b6048b1e02be5a4
Merge: 94432cc aee843a
Author: Kevin Murray <kdmfoss at gmail.com>
Date: Thu Dec 1 12:32:07 2016 +1100
Merge tag 'upstream/0.3.2+dfsg'
Upstream version 0.3.2+dfsg
.gitmodules | 3 -
.travis.yml | 38 +-
CMakeLists.txt | 42 +-
README.md | 8 +-
docs/gitversion.py | 4 +-
src/axe.c | 31 +-
src/axe.h | 13 +-
src/axe_config.h.in | 2 +
src/gsl/combination.c | 171 -
src/gsl/error.c | 77 -
src/gsl/gsl_combination.h | 76 -
src/gsl/gsl_errno.h | 153 -
src/gsl/gsl_message.h | 79 -
src/gsl/init.c | 127 -
src/gsl/message.c | 37 -
src/gsl/stream.c | 65 -
src/gsl/strerror.c | 100 -
src/libqes/.gitignore | 12 +
src/libqes/.gitmodules | 0
src/libqes/.travis.yml | 35 +
src/libqes/AUTHORS | 1 +
src/libqes/CMakeLists.txt | 147 +
src/libqes/LICENSE | 619 +++
src/libqes/README.md | 31 +
src/libqes/TODO.md | 11 +
src/libqes/cmake-modules/CodeCoverage.cmake | 158 +
src/libqes/cmake-modules/FindLIBQES.cmake | 97 +
.../cmake-modules/GetGitRevisionDescription.cmake | 130 +
.../GetGitRevisionDescription.cmake.in | 38 +
src/libqes/cmake-modules/GitSemVer.cmake | 49 +
src/libqes/src/CMakeLists.txt | 27 +
src/libqes/src/crc.c | 101 +
src/libqes/src/crc.h | 46 +
src/libqes/src/qes.h | 42 +
src/libqes/src/qes_compat.c | 82 +
src/libqes/src/qes_compat.h | 45 +
src/libqes/src/qes_config.h.in | 92 +
src/libqes/src/qes_file.c | 520 +++
src/libqes/src/qes_file.h | 229 ++
src/libqes/src/qes_libgnu.c | 32 +
src/libqes/src/qes_libgnu.h | 44 +
src/libqes/src/qes_log.c | 267 ++
src/libqes/src/qes_log.h | 166 +
src/libqes/src/qes_match.c | 99 +
src/libqes/src/qes_match.h | 66 +
src/libqes/src/qes_seq.c | 232 ++
src/libqes/src/qes_seq.h | 219 ++
src/libqes/src/qes_seqfile.c | 327 ++
src/libqes/src/qes_seqfile.h | 240 ++
src/libqes/src/qes_sequtil.c | 272 ++
src/libqes/src/qes_sequtil.h | 39 +
src/libqes/src/qes_str.c | 52 +
src/libqes/src/qes_str.h | 184 +
src/libqes/src/qes_util.c | 75 +
src/libqes/src/qes_util.h | 250 ++
src/libqes/test/CMakeLists.txt | 45 +
src/libqes/test/benchmarks.c | 311 ++
src/libqes/test/data/bad_diff_lens.fastq | 4 +
src/libqes/test/data/bad_nohdr.fastq | 3 +
src/libqes/test/data/bad_noqual.fastq | 3 +
src/libqes/test/data/bad_noqualhdrchr.fastq | 4 +
src/libqes/test/data/bad_noqualhdreol.fastq | 3 +
src/libqes/test/data/empty.fastq | 1 +
src/libqes/test/data/empty.txt | 0
src/libqes/test/data/loremipsum.txt | 11 +
src/libqes/test/data/loremipsum.txt.gz | Bin 0 -> 427 bytes
src/libqes/test/data/nocomment.fasta | 5 +
src/libqes/test/data/random.bin | Bin 0 -> 8192 bytes
src/libqes/test/data/test.fasta | 4061 ++++++++++++++++++++
src/libqes/test/data/test.fastq | 4000 +++++++++++++++++++
src/libqes/test/data/test.fastq.bz2 | Bin 0 -> 17766 bytes
src/libqes/test/data/test.fastq.gz | Bin 0 -> 24811 bytes
src/libqes/test/data/test_large.fasta.gz | Bin 0 -> 317571 bytes
src/libqes/test/data/truth/log_test.txt | 2 +
src/libqes/test/data/truth/qes_seq_print.fa | 2 +
src/libqes/test/data/truth/qes_seq_print.fq | 4 +
src/libqes/test/helpers.c | 207 +
src/libqes/test/helpers.h | 56 +
src/libqes/test/kseq.h | 235 ++
src/libqes/test/kseqcat.c | 41 +
src/libqes/test/logdemo.c | 50 +
src/libqes/test/qes_seqcat.c | 30 +
src/libqes/test/qes_seqprint.c | 21 +
src/libqes/test/test.c | 80 +
src/libqes/test/test_file.c | 446 +++
src/libqes/test/test_helpers.c | 70 +
src/libqes/test/test_log.c | 189 +
src/libqes/test/test_match.c | 105 +
src/libqes/test/test_seq.c | 500 +++
src/libqes/test/test_seqcats.sh | 34 +
src/libqes/test/test_seqfile.c | 418 ++
src/libqes/test/test_sequtil.c | 67 +
src/libqes/test/test_util.c | 161 +
src/libqes/test/testdata.c | 160 +
src/libqes/test/testdata.h | 65 +
src/libqes/test/tests.h | 57 +
src/libqes/test/tinytest/tinytest.c | 493 +++
src/libqes/test/tinytest/tinytest.h | 100 +
src/libqes/test/tinytest/tinytest_macros.h | 199 +
src/libqes/util/make_codon_list.py | 38 +
src/libqes/util/make_codon_map.py | 21 +
src/main.c | 137 +-
tests/CMakeLists.txt | 2 +-
utils/hbb_script.sh | 25 +
utils/make-tarball.sh | 19 -
utils/static_build.sh | 28 +
106 files changed, 17555 insertions(+), 1060 deletions(-)
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