[med-svn] [axe-demultiplexer] branch upstream updated (1b05416 -> 5fd41eb)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Oct 27 23:11:27 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch upstream
in repository axe-demultiplexer.
from 1b05416 Imported Upstream version 0.2.8
adds 5fd41eb Imported Upstream version 0.3.0+dfsg
No new revisions were added by this update.
Summary of changes:
.gitattributes | 1 +
.gitignore | 1 +
.gitmodules | 3 +
.travis.yml | 44 +-
CMakeLists.txt | 10 +-
README.md | 10 +-
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 +-
102 files changed, 363 insertions(+), 17391 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitmodules
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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