This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository pbgenomicconsensus.
commit 71dce5212fb7b0028ad501b78c2ef83384bafc1c Merge: 43f2095 da58626 Author: Afif Elghraoui <[email protected]> Date: Wed Feb 3 00:51:30 2016 -0800 Merge tag 'upstream/2.0.0+20151210' Upstream version 2.0.0+20151210 GenomicConsensus/ResultCollector.py | 6 +- GenomicConsensus/Worker.py | 2 +- GenomicConsensus/consensus.py | 6 +- GenomicConsensus/io/utils.py | 3 +- GenomicConsensus/main.py | 121 ++++++--- GenomicConsensus/options.py | 145 +++++++---- GenomicConsensus/plurality/plurality.py | 2 +- GenomicConsensus/quiver/model.py | 2 +- GenomicConsensus/quiver/quiver.py | 7 +- GenomicConsensus/quiver/utils.py | 2 +- GenomicConsensus/reference.py | 53 ++-- GenomicConsensus/utils.py | 61 ++++- README.md | 24 +- bin/gffToBed | 209 ++++++++++++++++ bin/gffToBed.py | 141 ----------- bin/{gffToVcf.py => gffToVcf} | 94 +++++-- bin/makePbi.py | 115 --------- bin/plurality | 2 +- bin/quiver | 2 +- bin/{summarizeConsensus.py => summarizeConsensus} | 114 +++++++-- bin/{variantCaller.py => variantCaller} | 0 doc/HowToQuiver.rst | 79 +++--- setup.py | 15 +- tests/cram/bad_input.t | 5 + tests/cram/extra/convert-to-bed.t | 4 +- tests/cram/extra/convert-to-vcf.t | 2 +- tests/cram/extra/coverage-bed.t | 4 +- tests/cram/extra/plurality-compressed.t | 2 +- tests/cram/extra/plurality-fluidigm.t | 2 +- tests/cram/internal/alignment_summary.t | 4 +- tests/cram/internal/quiver-compatibility.t | 4 +- tests/cram/internal/quiver-staph.t | 21 +- tests/cram/makePbi.t.off | 284 ---------------------- tests/cram/plurality-hcv.t | 2 +- tests/cram/version.t | 11 +- tests/unit/test_tool_contract.py | 82 +++++++ 36 files changed, 829 insertions(+), 803 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
