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commit 79935296187b3da5d645e09e24a383cb10c97fba Merge: b96def7 1067366 Author: Andreas Tille <[email protected]> Date: Thu Nov 16 09:33:46 2017 +0100 Updated version 1.2.12 from 'upstream/1.2.12' with Debian dir 04c7ca6383af2ebab1d25cff94d213d0b2405c83 .gitignore | 2 + CHANGES.md | 109 +++++- INSTALL.rst | 4 + README.rst | 16 +- docs/bam_pipeline/requirements.rst | 6 +- docs/conf.py | 28 +- docs/index.rst | 14 +- docs/yaml.rst | 164 ++++++++- docs/zonkey_pipeline/index.rst | 11 +- paleomix/__init__.py | 2 +- paleomix/atomiccmd/builder.py | 81 +++-- paleomix/atomiccmd/command.py | 8 +- paleomix/atomiccmd/pprint.py | 102 +++--- paleomix/common/formats/fasta.py | 16 +- paleomix/common/makefile.py | 20 ++ paleomix/common/testing.py | 6 +- paleomix/common/vcffilter.py | 3 +- paleomix/common/vcfwrap.py | 15 +- paleomix/common/versions.py | 77 +++-- paleomix/main.py | 4 + paleomix/node.py | 100 +++--- paleomix/nodes/bowtie2.py | 31 +- paleomix/nodes/bwa.py | 41 +-- paleomix/nodes/commands.py | 73 ++-- paleomix/nodes/mapdamage.py | 38 +- paleomix/nodes/picard.py | 233 ++++++------- paleomix/nodes/samtools.py | 27 +- paleomix/nodes/validation.py | 252 ++++++++------ paleomix/pipeline.py | 4 +- paleomix/tools/bam_pipeline/makefile.py | 105 +++--- paleomix/tools/bam_pipeline/mkfile.py | 6 +- paleomix/tools/bam_pipeline/nodes.py | 73 ++-- paleomix/tools/bam_pipeline/parts/lane.py | 9 +- paleomix/tools/bam_pipeline/parts/library.py | 40 ++- paleomix/tools/bam_pipeline/parts/prefix.py | 102 ++++-- paleomix/tools/bam_pipeline/parts/statistics.py | 20 +- paleomix/tools/bam_pipeline/pipeline.py | 46 ++- paleomix/tools/bam_stats/common.py | 2 +- paleomix/tools/cleanup.py | 42 ++- paleomix/tools/dupcheck.py | 93 +++++ paleomix/tools/rmdup_collapsed.py | 315 ++++++++++------- paleomix/tools/zonkey/config.py | 18 +- paleomix/tools/zonkey/pipeline.py | 17 +- paleomix/ui.py | 10 +- setup.py | 2 +- tests/.coveragerc | 11 + tests/README.md | 4 + tests/atomiccmd_test/builder_test.py | 75 +++- tests/atomiccmd_test/command_test.py | 213 +++++++----- tests/atomiccmd_test/pprint_test.py | 439 ++++++++++++++---------- tests/atomiccmd_test/sets_test.py | 18 +- tests/common_tests/fileutils_test.py | 10 +- tests/common_tests/makefile_test.py | 216 ++++++++++-- tests/common_tests/versions_tests.py | 118 +++++-- tests/run | 27 -- tests/setup.sh | 15 + tox.ini | 4 +- 57 files changed, 2286 insertions(+), 1251 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paleomix.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
