This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit 936f8790f28a19cde87d29fa59c0ed4b033d5cc2 Merge: 4cfbd03 381599a Author: Michael R. Crusoe <[email protected]> Date: Fri Sep 4 15:43:28 2015 -0700 Merge tag 'upstream/2.0_rc6+dfsg' Upstream version 2.0~rc6+dfsg .mailmap | 9 +- CITATION | 119 +++++-- CODE_OF_CONDUCT.rst | 38 +++ CONTRIBUTING.md | 39 +++ ChangeLog | 176 ++++++++++ Doxyfile.in | 21 +- LICENSE | 141 ++++++-- MANIFEST.in | 2 +- Makefile | 74 ++++- README.rst | 38 +++ bink.ipynb | 535 ------------------------------ doc/LICENSE.rst | 3 +- doc/_static/labibi.css | 2 +- doc/conf.py | 7 +- doc/contributors.rst | 53 ++- doc/dev/a-quick-guide-to-testing.rst | 38 +++ doc/dev/binary-file-formats.rst | 44 ++- doc/dev/codebase-guide.rst | 50 ++- doc/dev/coding-guidelines-and-review.rst | 47 ++- doc/dev/crazy-ideas.rst | 39 ++- doc/dev/details.rst | 37 ++- doc/dev/development.rst | 59 +++- doc/dev/for-khmer-developers.rst | 42 ++- doc/dev/getting-started.rst | 157 ++++++++- doc/dev/hackathon.rst | 37 +++ doc/dev/index.rst | 38 +++ doc/dev/release.rst | 42 ++- doc/dev/scripts-and-sandbox.rst | 58 +++- doc/index.rst | 144 ++++++-- doc/introduction.rst | 63 +++- doc/release-notes/index.rst | 39 +++ doc/release-notes/release-1.0.1.md | 38 +++ doc/release-notes/release-1.0.1.rst | 40 +++ doc/release-notes/release-1.0.md | 38 +++ doc/release-notes/release-1.0.rst | 40 +++ doc/release-notes/release-1.1.md | 38 +++ doc/release-notes/release-1.1.rst | 40 +++ doc/release-notes/release-1.2.md | 38 +++ doc/release-notes/release-1.2.rst | 40 +++ doc/release-notes/release-1.3.md | 37 +++ doc/release-notes/release-1.3.rst | 40 +++ doc/release-notes/release-1.4.md | 39 ++- doc/release-notes/release-1.4.rst | 40 +++ doc/release-notes/release-2.0.md | 340 +++++++++++++++++++ doc/release-notes/release-2.0.rst | 386 +++++++++++++++++++++ doc/requirements.txt | 2 +- doc/roadmap.rst | 38 ++- doc/run-corn-50m.sh | 41 ++- doc/user/biblio.rst | 72 +++- doc/user/blog-posts.rst | 40 ++- doc/user/choosing-table-sizes.rst | 73 +++- doc/user/examples.rst | 55 ++- doc/user/galaxy.rst | 48 ++- doc/user/getting-help.rst | 43 ++- doc/user/guide.rst | 159 ++++----- doc/user/index.rst | 38 +++ doc/user/install.rst | 46 ++- doc/user/known-issues.rst | 47 ++- doc/user/partitioning-big-data.rst | 42 ++- doc/user/scripts.rst | 61 +++- doc/whats-new-2.0.rst | 184 ++++++++-- examples/stamps/do.sh | 34 +- ez_setup.py | 332 ------------------ jenkins-build.sh | 34 ++ khmer/__init__.py | 37 ++- khmer/_khmer.cc | 60 +++- khmer/_version.py | 4 +- khmer/kfile.py | 37 ++- khmer/khmer_args.py | 60 +++- khmer/khmer_logger.py | 37 ++- khmer/thread_utils.py | 49 ++- khmer/utils.py | 43 ++- lib/.check_openmp.cc | 42 ++- lib/Makefile | 58 +++- lib/counting.cc | 52 ++- lib/counting.hh | 50 ++- lib/get_version.py | 42 ++- lib/graphtest.cc | 80 ----- lib/hashbits.cc | 44 ++- lib/hashbits.hh | 48 ++- lib/hashtable.cc | 102 ++++-- lib/hashtable.hh | 51 ++- lib/hllcounter.cc | 52 ++- lib/hllcounter.hh | 46 ++- lib/khmer.hh | 44 ++- lib/khmer_exception.hh | 44 ++- lib/kmer_hash.cc | 48 ++- lib/kmer_hash.hh | 75 +++-- lib/labelhash.cc | 44 ++- lib/labelhash.hh | 46 ++- lib/primes.hh | 75 ----- lib/read_aligner.cc | 42 ++- lib/read_aligner.hh | 43 ++- lib/read_aligner_test.sh | 1 - lib/read_parsers.cc | 44 ++- lib/read_parsers.hh | 44 ++- lib/subset.cc | 70 +++- lib/subset.hh | 44 ++- lib/test-Colors.cc | 42 ++- lib/test-compile.cc | 46 ++- lib/test-read-aligner.cc | 63 ---- lib/traversal.cc | 47 ++- lib/traversal.hh | 48 ++- oxli/__init__.py | 55 ++- oxli/build_graph.py | 39 ++- oxli/functions.py | 43 ++- sandbox/Makefile.read_aligner_training | 35 ++ sandbox/README.rst | 38 +++ sandbox/abundance-hist-by-position.py | 36 +- sandbox/assembly-diff-2.py | 36 +- sandbox/assembly-diff.py | 36 +- sandbox/assemstats3.py | 48 ++- sandbox/bloom-count.py | 40 ++- sandbox/build-sparse-graph.py | 39 ++- sandbox/calc-best-assembly.py | 35 +- sandbox/calc-error-profile.py | 37 ++- sandbox/calc-median-distribution.py | 36 +- sandbox/collect-reads.py | 39 ++- sandbox/collect-variants.py | 36 +- sandbox/correct-reads.py | 45 ++- sandbox/count-kmers-single.py | 37 ++- sandbox/count-kmers.py | 37 ++- sandbox/error-correct-pass2.py | 38 ++- sandbox/estimate_optimal_hash.py | 42 ++- sandbox/extract-single-partition.py | 36 +- sandbox/fasta-to-abundance-hist.py | 36 +- sandbox/filter-below-abund.py | 36 +- sandbox/filter-median-and-pct.py | 36 +- sandbox/filter-median.py | 36 +- sandbox/find-high-abund-kmers.py | 39 ++- sandbox/graph-size.py | 36 +- sandbox/hi-lo-abundance-by-position.py | 36 +- sandbox/make-coverage.py | 37 ++- sandbox/memusg | 46 --- sandbox/multi-rename.py | 37 ++- sandbox/normalize-by-median-pct.py | 38 ++- sandbox/optimal_args_hashbits.py | 38 ++- sandbox/print-stoptags.py | 36 +- sandbox/print-tagset.py | 36 +- sandbox/readaligner_pairhmm_train.py | 34 ++ sandbox/renumber-partitions.py | 36 +- sandbox/saturate-by-median.py | 43 ++- sandbox/shuffle-reverse-rotary.py | 38 ++- sandbox/slice-reads-by-coverage.py | 35 +- sandbox/split-fasta.py | 36 +- sandbox/split-sequences-by-length.py | 38 ++- sandbox/stoptag-abundance-hist.py | 36 +- sandbox/stoptags-by-position.py | 38 ++- sandbox/strip-partition.py | 36 +- sandbox/subset-report.py | 36 +- sandbox/sweep-files.py | 40 ++- sandbox/sweep-out-reads-with-contigs.py | 37 ++- sandbox/sweep-reads.py | 42 ++- sandbox/sweep-reads2.py | 36 +- sandbox/sweep-reads3.py | 36 +- sandbox/write-trimmomatic.py | 37 ++- scripts/README.txt | 1 - scripts/abundance-dist-single.py | 58 +++- scripts/abundance-dist.py | 58 +++- scripts/annotate-partitions.py | 62 +++- scripts/count-median.py | 59 +++- scripts/do-partition.py | 63 +++- scripts/extract-long-sequences.py | 52 ++- scripts/extract-paired-reads.py | 59 +++- scripts/extract-partitions.py | 59 +++- scripts/fastq-to-fasta.py | 46 ++- scripts/filter-abund-single.py | 50 ++- scripts/filter-abund.py | 52 ++- scripts/filter-stoptags.py | 60 +++- scripts/find-knots.py | 59 +++- scripts/interleave-reads.py | 57 +++- scripts/load-graph.py | 39 ++- scripts/load-into-counting.py | 61 +++- scripts/make-initial-stoptags.py | 55 ++- scripts/merge-partitions.py | 55 ++- scripts/normalize-by-median.py | 75 +++-- scripts/oxli | 35 +- scripts/partition-graph.py | 63 +++- scripts/readstats.py | 55 ++- scripts/sample-reads-randomly.py | 66 +++- scripts/split-paired-reads.py | 53 ++- scripts/trim-low-abund.py | 58 +++- scripts/unique-kmers.py | 57 +++- setup.py | 73 +++- sort-authors-list.py | 92 +++++ tests/__init__.py | 35 +- tests/khmer_tst_utils.py | 42 ++- tests/test_countgraph.py | 40 ++- tests/test_counting_single.py | 41 ++- tests/test_filter.py | 40 ++- tests/test_functions.py | 40 ++- tests/test_graph.py | 40 ++- tests/test_hll.py | 40 ++- tests/test_labelhash.py | 40 ++- tests/test_lump.py | 38 ++- tests/test_nodegraph.py | 36 +- tests/test_normalize_by_median.py | 49 ++- tests/test_oxli_functions.py | 42 ++- tests/test_read_aligner.py | 40 ++- tests/test_read_parsers.py | 42 ++- tests/test_sandbox_scripts.py | 36 +- tests/test_script_arguments.py | 36 +- tests/test_scripts.py | 195 ++++++----- tests/test_streaming_io.py | 39 ++- tests/test_subset_graph.py | 40 ++- tests/test_threaded_sequence_processor.py | 66 +++- tests/test_version.py | 38 ++- versioneer.py | 0 208 files changed, 8744 insertions(+), 2641 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
