[med-svn] [axe-demultiplexer] branch master updated (94432cc -> 0554585)
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Dec 1 01:52:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository axe-demultiplexer.
from 94432cc s/UNRELEASED/unstable/
new aee843a New upstream version 0.3.2+dfsg
new 5e8a9e7 Merge tag 'upstream/0.3.2+dfsg'
new 35ce036 Bump changelog
new 5613990 Refresh patches
new 6fd9662 Bump standards version
new 0554585 Fix dynamic linking to libqes
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:
.gitmodules | 3 -
.travis.yml | 38 +-
CMakeLists.txt | 42 +-
README.md | 8 +-
debian/changelog | 7 +
debian/control | 2 +-
.../patches/0002-Remove-libqes-from-CML.txt.patch | 11 +-
...-Use-standard-include-path-of-gsl-headers.patch | 2 +-
.../patches/0004-Dynamically-link-to-libqes.patch | 18 +-
debian/patches/cmake-version | 12 +-
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 -
.gitignore => src/libqes/.gitignore | 1 -
src/libqes/.gitmodules | 0
src/libqes/.travis.yml | 35 +
src/libqes/AUTHORS | 1 +
src/libqes/CMakeLists.txt | 147 +
LICENSE.txt => src/libqes/LICENSE | 0
src/libqes/README.md | 31 +
src/libqes/TODO.md | 11 +
src/libqes/cmake-modules/CodeCoverage.cmake | 158 +
.../libqes/cmake-modules}/FindLIBQES.cmake | 36 +-
.../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 +
{tests => src/libqes/test}/tinytest/tinytest.c | 12 +-
{tests => src/libqes/test}/tinytest/tinytest.h | 0
.../libqes/test}/tinytest/tinytest_macros.h | 2 +-
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 +
112 files changed, 16104 insertions(+), 1094 deletions(-)
delete mode 100644 .gitmodules
delete mode 100644 src/gsl/combination.c
delete mode 100644 src/gsl/error.c
delete mode 100644 src/gsl/gsl_combination.h
delete mode 100644 src/gsl/gsl_errno.h
delete mode 100644 src/gsl/gsl_message.h
delete mode 100644 src/gsl/init.c
delete mode 100644 src/gsl/message.c
delete mode 100644 src/gsl/stream.c
delete mode 100644 src/gsl/strerror.c
copy .gitignore => src/libqes/.gitignore (92%)
create mode 100644 src/libqes/.gitmodules
create mode 100644 src/libqes/.travis.yml
create mode 100644 src/libqes/AUTHORS
create mode 100644 src/libqes/CMakeLists.txt
copy LICENSE.txt => src/libqes/LICENSE (100%)
create mode 100644 src/libqes/README.md
create mode 100644 src/libqes/TODO.md
create mode 100644 src/libqes/cmake-modules/CodeCoverage.cmake
copy {cmake-modules => src/libqes/cmake-modules}/FindLIBQES.cmake (65%)
create mode 100644 src/libqes/cmake-modules/GetGitRevisionDescription.cmake
create mode 100644 src/libqes/cmake-modules/GetGitRevisionDescription.cmake.in
create mode 100644 src/libqes/cmake-modules/GitSemVer.cmake
create mode 100644 src/libqes/src/CMakeLists.txt
create mode 100644 src/libqes/src/crc.c
create mode 100644 src/libqes/src/crc.h
create mode 100644 src/libqes/src/qes.h
create mode 100644 src/libqes/src/qes_compat.c
create mode 100644 src/libqes/src/qes_compat.h
create mode 100644 src/libqes/src/qes_config.h.in
create mode 100644 src/libqes/src/qes_file.c
create mode 100644 src/libqes/src/qes_file.h
create mode 100644 src/libqes/src/qes_libgnu.c
create mode 100644 src/libqes/src/qes_libgnu.h
create mode 100644 src/libqes/src/qes_log.c
create mode 100644 src/libqes/src/qes_log.h
create mode 100644 src/libqes/src/qes_match.c
create mode 100644 src/libqes/src/qes_match.h
create mode 100644 src/libqes/src/qes_seq.c
create mode 100644 src/libqes/src/qes_seq.h
create mode 100644 src/libqes/src/qes_seqfile.c
create mode 100644 src/libqes/src/qes_seqfile.h
create mode 100644 src/libqes/src/qes_sequtil.c
create mode 100644 src/libqes/src/qes_sequtil.h
create mode 100644 src/libqes/src/qes_str.c
create mode 100644 src/libqes/src/qes_str.h
create mode 100644 src/libqes/src/qes_util.c
create mode 100644 src/libqes/src/qes_util.h
create mode 100644 src/libqes/test/CMakeLists.txt
create mode 100644 src/libqes/test/benchmarks.c
create mode 100644 src/libqes/test/data/bad_diff_lens.fastq
create mode 100644 src/libqes/test/data/bad_nohdr.fastq
create mode 100644 src/libqes/test/data/bad_noqual.fastq
create mode 100644 src/libqes/test/data/bad_noqualhdrchr.fastq
create mode 100644 src/libqes/test/data/bad_noqualhdreol.fastq
create mode 100644 src/libqes/test/data/empty.fastq
create mode 100644 src/libqes/test/data/empty.txt
create mode 100644 src/libqes/test/data/loremipsum.txt
create mode 100644 src/libqes/test/data/loremipsum.txt.gz
create mode 100644 src/libqes/test/data/nocomment.fasta
create mode 100644 src/libqes/test/data/random.bin
create mode 100644 src/libqes/test/data/test.fasta
create mode 100644 src/libqes/test/data/test.fastq
create mode 100644 src/libqes/test/data/test.fastq.bz2
create mode 100644 src/libqes/test/data/test.fastq.gz
create mode 100644 src/libqes/test/data/test_large.fasta.gz
create mode 100644 src/libqes/test/data/truth/log_test.txt
create mode 100644 src/libqes/test/data/truth/qes_seq_print.fa
create mode 100644 src/libqes/test/data/truth/qes_seq_print.fq
create mode 100644 src/libqes/test/helpers.c
create mode 100644 src/libqes/test/helpers.h
create mode 100644 src/libqes/test/kseq.h
create mode 100644 src/libqes/test/kseqcat.c
create mode 100644 src/libqes/test/logdemo.c
create mode 100644 src/libqes/test/qes_seqcat.c
create mode 100644 src/libqes/test/qes_seqprint.c
create mode 100644 src/libqes/test/test.c
create mode 100644 src/libqes/test/test_file.c
create mode 100644 src/libqes/test/test_helpers.c
create mode 100644 src/libqes/test/test_log.c
create mode 100644 src/libqes/test/test_match.c
create mode 100644 src/libqes/test/test_seq.c
create mode 100644 src/libqes/test/test_seqcats.sh
create mode 100644 src/libqes/test/test_seqfile.c
create mode 100644 src/libqes/test/test_sequtil.c
create mode 100644 src/libqes/test/test_util.c
create mode 100644 src/libqes/test/testdata.c
create mode 100644 src/libqes/test/testdata.h
create mode 100644 src/libqes/test/tests.h
copy {tests => src/libqes/test}/tinytest/tinytest.c (98%)
copy {tests => src/libqes/test}/tinytest/tinytest.h (100%)
copy {tests => src/libqes/test}/tinytest/tinytest_macros.h (99%)
create mode 100644 src/libqes/util/make_codon_list.py
create mode 100644 src/libqes/util/make_codon_map.py
create mode 100644 utils/hbb_script.sh
delete mode 100644 utils/make-tarball.sh
create mode 100644 utils/static_build.sh
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