[med-svn] [axe-demultiplexer] branch master updated (51be2b6 -> 500b34c)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Oct 27 22:06:23 UTC 2015
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 51be2b6 Add dfsg suffix to d/watch
new 5fd41eb Imported Upstream version 0.3.0+dfsg
new 2022821 Merge tag 'upstream/0.3.0+dfsg'
new b1c4dce Drop spell-checking patch
new 500b34c Use --parallel to dh in d/rules
The 4 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:
.gitattributes | 1 +
.gitignore | 1 +
.gitmodules | 3 +
.travis.yml | 44 +-
CMakeLists.txt | 10 +-
README.md | 10 +-
.../patches/0002-Fix-typo-seperate-separate.patch | 24 -
debian/patches/series | 1 -
debian/rules | 2 +-
docs/CMakeLists.txt | 2 +
docs/conf.py | 7 +-
docs/gitversion.py | 189 +
docs/usage.rst | 9 +-
docs/usage.txt | 6 +-
src/CMakeLists.txt | 30 +-
src/axe.c | 20 +-
src/axe.h | 31 +-
src/axe_config.h.in | 18 +-
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/.travis.yml | 38 -
src/libqes/AUTHORS | 1 -
src/libqes/CMakeLists.txt | 154 -
src/libqes/LICENSE | 619 ---
src/libqes/README.md | 31 -
src/libqes/cmake-modules/CodeCoverage.cmake | 158 -
src/libqes/cmake-modules/FindLIBQES.cmake | 83 -
.../cmake-modules/GetGitRevisionDescription.cmake | 130 -
.../GetGitRevisionDescription.cmake.in | 38 -
src/libqes/cmake-modules/GitSemVer.cmake | 27 -
src/libqes/src/CMakeLists.txt | 16 -
src/libqes/src/crc.c | 101 -
src/libqes/src/crc.h | 46 -
src/libqes/src/qes.h | 26 -
src/libqes/src/qes_compat.c | 66 -
src/libqes/src/qes_compat.h | 29 -
src/libqes/src/qes_config.h.in | 76 -
src/libqes/src/qes_file.c | 496 ---
src/libqes/src/qes_file.h | 213 -
src/libqes/src/qes_libgnu.c | 16 -
src/libqes/src/qes_libgnu.h | 28 -
src/libqes/src/qes_log.c | 251 --
src/libqes/src/qes_log.h | 150 -
src/libqes/src/qes_match.c | 83 -
src/libqes/src/qes_match.h | 50 -
src/libqes/src/qes_seq.c | 157 -
src/libqes/src/qes_seq.h | 187 -
src/libqes/src/qes_seqfile.c | 319 --
src/libqes/src/qes_seqfile.h | 224 --
src/libqes/src/qes_sequtil.c | 256 --
src/libqes/src/qes_sequtil.h | 23 -
src/libqes/src/qes_str.c | 36 -
src/libqes/src/qes_str.h | 135 -
src/libqes/src/qes_util.c | 59 -
src/libqes/src/qes_util.h | 236 --
src/libqes/test/CMakeLists.txt | 36 -
src/libqes/test/benchmarks.c | 295 --
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/log_test.txt | 2 -
src/libqes/test/data/loremipsum.txt | 11 -
src/libqes/test/data/loremipsum.txt.gz | Bin 427 -> 0 bytes
src/libqes/test/data/nocomment.fasta | 5 -
src/libqes/test/data/random.bin | Bin 8192 -> 0 bytes
src/libqes/test/data/test.fasta | 4061 --------------------
src/libqes/test/data/test.fastq | 4000 -------------------
src/libqes/test/data/test.fastq.bz2 | Bin 17766 -> 0 bytes
src/libqes/test/data/test.fastq.gz | Bin 24811 -> 0 bytes
src/libqes/test/helpers.c | 191 -
src/libqes/test/helpers.h | 40 -
src/libqes/test/kseq.h | 235 --
src/libqes/test/logdemo.c | 34 -
src/libqes/test/test.c | 64 -
src/libqes/test/test_file.c | 430 ---
src/libqes/test/test_helpers.c | 54 -
src/libqes/test/test_log.c | 173 -
src/libqes/test/test_match.c | 89 -
src/libqes/test/test_seq.c | 422 --
src/libqes/test/test_seqfile.c | 402 --
src/libqes/test/test_sequtil.c | 51 -
src/libqes/test/test_util.c | 145 -
src/libqes/test/testdata.c | 144 -
src/libqes/test/testdata.h | 49 -
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 | 32 +-
tests/CMakeLists.txt | 4 +-
tests/{axe_integration.py => axe_cli_tests.py} | 23 +-
105 files changed, 364 insertions(+), 17417 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitmodules
delete mode 100644 debian/patches/0002-Fix-typo-seperate-separate.patch
create mode 100644 docs/gitversion.py
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
delete mode 100644 src/libqes/.gitignore
delete mode 100644 src/libqes/.travis.yml
delete mode 100644 src/libqes/AUTHORS
delete mode 100644 src/libqes/CMakeLists.txt
delete mode 100644 src/libqes/LICENSE
delete mode 100644 src/libqes/README.md
delete mode 100644 src/libqes/cmake-modules/CodeCoverage.cmake
delete mode 100644 src/libqes/cmake-modules/FindLIBQES.cmake
delete mode 100644 src/libqes/cmake-modules/GetGitRevisionDescription.cmake
delete mode 100644 src/libqes/cmake-modules/GetGitRevisionDescription.cmake.in
delete mode 100644 src/libqes/cmake-modules/GitSemVer.cmake
delete mode 100644 src/libqes/src/CMakeLists.txt
delete mode 100644 src/libqes/src/crc.c
delete mode 100644 src/libqes/src/crc.h
delete mode 100644 src/libqes/src/qes.h
delete mode 100644 src/libqes/src/qes_compat.c
delete mode 100644 src/libqes/src/qes_compat.h
delete mode 100644 src/libqes/src/qes_config.h.in
delete mode 100644 src/libqes/src/qes_file.c
delete mode 100644 src/libqes/src/qes_file.h
delete mode 100644 src/libqes/src/qes_libgnu.c
delete mode 100644 src/libqes/src/qes_libgnu.h
delete mode 100644 src/libqes/src/qes_log.c
delete mode 100644 src/libqes/src/qes_log.h
delete mode 100644 src/libqes/src/qes_match.c
delete mode 100644 src/libqes/src/qes_match.h
delete mode 100644 src/libqes/src/qes_seq.c
delete mode 100644 src/libqes/src/qes_seq.h
delete mode 100644 src/libqes/src/qes_seqfile.c
delete mode 100644 src/libqes/src/qes_seqfile.h
delete mode 100644 src/libqes/src/qes_sequtil.c
delete mode 100644 src/libqes/src/qes_sequtil.h
delete mode 100644 src/libqes/src/qes_str.c
delete mode 100644 src/libqes/src/qes_str.h
delete mode 100644 src/libqes/src/qes_util.c
delete mode 100644 src/libqes/src/qes_util.h
delete mode 100644 src/libqes/test/CMakeLists.txt
delete mode 100644 src/libqes/test/benchmarks.c
delete mode 100644 src/libqes/test/data/bad_diff_lens.fastq
delete mode 100644 src/libqes/test/data/bad_nohdr.fastq
delete mode 100644 src/libqes/test/data/bad_noqual.fastq
delete mode 100644 src/libqes/test/data/bad_noqualhdrchr.fastq
delete mode 100644 src/libqes/test/data/bad_noqualhdreol.fastq
delete mode 100644 src/libqes/test/data/empty.fastq
delete mode 100644 src/libqes/test/data/empty.txt
delete mode 100644 src/libqes/test/data/log_test.txt
delete mode 100644 src/libqes/test/data/loremipsum.txt
delete mode 100644 src/libqes/test/data/loremipsum.txt.gz
delete mode 100644 src/libqes/test/data/nocomment.fasta
delete mode 100644 src/libqes/test/data/random.bin
delete mode 100644 src/libqes/test/data/test.fasta
delete mode 100644 src/libqes/test/data/test.fastq
delete mode 100644 src/libqes/test/data/test.fastq.bz2
delete mode 100644 src/libqes/test/data/test.fastq.gz
delete mode 100644 src/libqes/test/helpers.c
delete mode 100644 src/libqes/test/helpers.h
delete mode 100644 src/libqes/test/kseq.h
delete mode 100644 src/libqes/test/logdemo.c
delete mode 100644 src/libqes/test/test.c
delete mode 100644 src/libqes/test/test_file.c
delete mode 100644 src/libqes/test/test_helpers.c
delete mode 100644 src/libqes/test/test_log.c
delete mode 100644 src/libqes/test/test_match.c
delete mode 100644 src/libqes/test/test_seq.c
delete mode 100644 src/libqes/test/test_seqfile.c
delete mode 100644 src/libqes/test/test_sequtil.c
delete mode 100644 src/libqes/test/test_util.c
delete mode 100644 src/libqes/test/testdata.c
delete mode 100644 src/libqes/test/testdata.h
delete mode 100644 src/libqes/test/tests.h
delete mode 100644 src/libqes/test/tinytest/tinytest.c
delete mode 100644 src/libqes/test/tinytest/tinytest.h
delete mode 100644 src/libqes/test/tinytest/tinytest_macros.h
delete mode 100644 src/libqes/util/make_codon_list.py
delete mode 100644 src/libqes/util/make_codon_map.py
rename tests/{axe_integration.py => axe_cli_tests.py} (92%)
mode change 100644 => 100755
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