[med-svn] [khmer] 02/04: Merge tag 'upstream/2.0_rc6+dfsg'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Sep 4 23:11:50 UTC 2015
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 <crusoe at ucdavis.edu>
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(-)
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