[med-svn] [khmer] 02/06: Merge tag 'upstream/1.4+dfsg'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu May 28 00:34:06 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 ce38967d0d5c369b1245d66dc4b26a374fc6f3eb
Merge: cdd3ca1 f031ff0
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue May 26 16:44:24 2015 -0400
Merge tag 'upstream/1.4+dfsg'
Upstream version 1.4+dfsg
.gitignore | 3 +
CONTRIBUTING.md | 2 +
ChangeLog | 712 ++++-
Doxyfile.in | 2 +-
Makefile | 90 +-
README.rst | 23 +-
doc/{LICENSE.txt => LICENSE.rst} | 0
doc/README.html | 403 ---
doc/{citations.txt => citations.rst} | 0
doc/conf.py | 25 +-
doc/{contributors.txt => contributors.rst} | 0
.../{CODE_OF_CONDUCT.txt => CODE_OF_CONDUCT.rst} | 0
...to-testing.txt => a-quick-guide-to-testing.rst} | 5 +
doc/dev/{codebase-guide.txt => codebase-guide.rst} | 0
...review.txt => coding-guidelines-and-review.rst} | 39 +-
doc/dev/{crazy-ideas.txt => crazy-ideas.rst} | 0
doc/dev/{details.txt => details.rst} | 0
doc/dev/{development.txt => development.rst} | 0
...mer-developers.txt => for-khmer-developers.rst} | 0
.../{getting-started.txt => getting-started.rst} | 68 +-
doc/dev/{hackathon.txt => hackathon.rst} | 0
doc/dev/{index.txt => index.rst} | 3 +-
doc/dev/{release.txt => release.rst} | 17 +-
doc/dev/scripts-and-sandbox.rst | 120 +
doc/{index.txt => index.rst} | 8 +-
doc/introduction.rst | 99 +
doc/introduction.txt | 93 -
doc/release-notes/index.rst | 12 +
doc/release-notes/release-1.0.1.md | 2 +
doc/release-notes/release-1.0.1.rst | 71 +
doc/release-notes/release-1.0.md | 2 +
doc/release-notes/release-1.0.rst | 110 +
doc/release-notes/release-1.1.md | 2 +
doc/release-notes/release-1.1.rst | 77 +
doc/release-notes/release-1.2.md | 12 +-
doc/release-notes/release-1.2.rst | 106 +
doc/release-notes/release-1.3.md | 2 +
doc/release-notes/release-1.3.rst | 62 +
doc/release-notes/release-1.4.md | 237 ++
doc/release-notes/release-1.4.rst | 257 ++
doc/requirements.txt | 1 +
doc/{roadmap.txt => roadmap.rst} | 0
doc/user/{biblio.txt => biblio.rst} | 0
doc/user/{blog-posts.txt => blog-posts.rst} | 10 +-
...ng-table-sizes.txt => choosing-table-sizes.rst} | 8 +-
doc/user/{examples.txt => examples.rst} | 0
doc/user/{galaxy.txt => galaxy.rst} | 0
doc/user/getting-help.rst | 54 +
doc/user/{guide.txt => guide.rst} | 6 +-
doc/user/{index.txt => index.rst} | 1 +
doc/user/{install.txt => install.rst} | 4 +-
doc/user/{known-issues.txt => known-issues.rst} | 0
...ning-big-data.txt => partitioning-big-data.rst} | 0
doc/user/{scripts.txt => scripts.rst} | 6 +
examples/stamps/do.sh | 44 +-
jenkins-build.sh | 14 +-
khmer/__init__.py | 131 +-
khmer/_khmermodule.cc | 2758 ++++++++++++--------
khmer/_version.py | 110 +-
khmer/{file.py => kfile.py} | 66 +-
khmer/khmer_args.py | 31 +-
khmer/load_pe.py | 53 -
khmer/thread_utils.py | 28 +-
khmer/utils.py | 155 +-
lib/.check_openmp.cc | 17 +
lib/.gitignore | 11 +-
lib/Makefile | 342 ++-
lib/counting.cc | 118 +-
lib/counting.hh | 16 +-
lib/get_version.py | 22 +-
lib/graphtest.cc | 2 +-
lib/hashbits.cc | 55 +-
lib/hashbits.hh | 14 +-
lib/hashtable.cc | 138 +-
lib/hashtable.hh | 33 +-
lib/hllcounter.cc | 461 ++++
lib/hllcounter.hh | 221 ++
lib/ht-diff.cc | 2 +-
lib/khmer.hh | 7 +-
lib/khmer.pc.in | 14 +
lib/khmer_exception.hh | 37 +-
lib/kmer_hash.cc | 66 +-
lib/kmer_hash.hh | 10 +-
lib/labelhash.cc | 2 +-
lib/labelhash.hh | 2 +-
lib/perf_metrics.cc | 2 +-
lib/perf_metrics.hh | 2 +-
lib/primes.hh | 2 +-
lib/read_aligner.cc | 4 +-
lib/read_aligner.hh | 2 +-
lib/read_parsers.cc | 60 +-
lib/read_parsers.hh | 44 +-
lib/subset.cc | 23 +-
lib/subset.hh | 2 +-
lib/test-CacheManager.cc | 189 --
lib/test-Colors.cc | 2 +-
lib/test-HashTables.cc | 2 +-
lib/test-Parser.cc | 2 +-
lib/test-StreamReader.cc | 173 --
lib/test-compile.cc | 17 +
lib/{test_read_aligner.cc => test-read-aligner.cc} | 4 +-
lib/trace_logger.cc | 2 +-
lib/trace_logger.hh | 2 +-
sandbox/README.rst | 56 +-
sandbox/abundance-hist-by-position.py | 2 +-
sandbox/assembly-diff-2.py | 2 +-
sandbox/assembly-diff.py | 2 +-
sandbox/assemstats3.py | 2 +-
...intersection.py => bloom-count-intersection.py} | 2 +-
sandbox/{bloom_count.py => bloom-count.py} | 2 +-
sandbox/build-sparse-graph.py | 2 +-
sandbox/calc-best-assembly.py | 6 +-
sandbox/calc-error-profile.py | 6 +-
sandbox/calc-median-distribution.py | 2 +-
sandbox/collect-reads.py | 29 +-
sandbox/collect-variants.py | 13 +-
sandbox/combine-pe.py | 66 -
sandbox/compare-partitions.py | 68 -
sandbox/correct-errors.py | 21 +-
sandbox/count-within-radius.py | 60 -
sandbox/degree-by-position.py | 47 -
sandbox/dn-identify-errors.py | 147 --
sandbox/ec.py | 60 -
sandbox/error-correct-pass2.py | 85 -
sandbox/extract-single-partition.py | 2 +-
sandbox/fasta-to-abundance-hist.py | 2 +-
sandbox/filter-below-abund.py | 2 +-
sandbox/filter-median-and-pct.py | 4 +-
sandbox/filter-median.py | 4 +-
sandbox/find-high-abund-kmers.py | 2 +-
sandbox/find-unpart.py | 53 -
sandbox/graph-size.py | 2 +-
sandbox/hi-lo-abundance-by-position.py | 2 +-
sandbox/make-coverage.py | 47 +
sandbox/multi-rename.py | 2 +-
sandbox/normalize-by-align.py | 150 --
sandbox/normalize-by-median-pct.py | 6 +-
sandbox/print-stoptags.py | 2 +-
sandbox/print-tagset.py | 2 +-
sandbox/read_aligner.py | 64 -
sandbox/readstats.py | 51 -
sandbox/renumber-partitions.py | 2 +-
sandbox/saturate-by-median.py | 27 +-
sandbox/shuffle-fasta.py | 27 -
sandbox/shuffle-reverse-rotary.py | 2 +-
sandbox/slice-reads-by-coverage.py | 11 +-
sandbox/split-fasta.py | 2 +-
sandbox/split-sequences-by-length.py | 4 +-
sandbox/stoptag-abundance-hist.py | 2 +-
sandbox/stoptags-by-position.py | 2 +-
sandbox/strip-partition.py | 2 +-
sandbox/subset-report.py | 2 +-
sandbox/sweep-files.py | 10 +-
sandbox/sweep-out-reads-with-contigs.py | 2 +-
sandbox/sweep-reads.py | 38 +-
sandbox/sweep-reads2.py | 2 +-
sandbox/sweep-reads3.py | 6 +-
sandbox/to-casava-1.8-fastq.py | 61 -
sandbox/trim-low-abund.py | 236 --
sandbox/uniqify-sequences.py | 67 -
sandbox/unique-kmers.py | 96 +
sandbox/write-interleave.py | 29 -
sandbox/write-trimmomatic.py | 2 +-
scripts/abundance-dist-single.py | 29 +-
scripts/abundance-dist.py | 35 +-
scripts/annotate-partitions.py | 14 +-
scripts/count-median.py | 58 +-
scripts/count-overlap.py | 29 +-
scripts/do-partition.py | 24 +-
scripts/extract-long-sequences.py | 24 +-
scripts/extract-paired-reads.py | 83 +-
scripts/extract-partitions.py | 30 +-
scripts/fastq-to-fasta.py | 5 +-
scripts/filter-abund-single.py | 14 +-
scripts/filter-abund.py | 21 +-
scripts/filter-stoptags.py | 14 +-
scripts/find-knots.py | 17 +-
scripts/galaxy/gedlab.py | 4 +-
scripts/interleave-reads.py | 65 +-
scripts/load-graph.py | 23 +-
scripts/load-into-counting.py | 54 +-
scripts/make-initial-stoptags.py | 8 +-
scripts/merge-partitions.py | 12 +-
scripts/normalize-by-median.py | 215 +-
scripts/partition-graph.py | 14 +-
scripts/readstats.py | 184 ++
scripts/sample-reads-randomly.py | 73 +-
scripts/split-paired-reads.py | 125 +-
scripts/trim-low-abund.py | 331 +++
setup.cfg | 4 +-
setup.py | 92 +-
tests/khmer_tst_utils.py | 14 +-
.../{badversion-k12.kh => badversion-k12.ct} | Bin
tests/test-data/casava_18-pe.fq | 16 +
tests/test-data/{normC20k20.kh => normC20k20.ct} | Bin
...-mixed.fq.pe => old-style-format-w-comments.fq} | 12 +-
tests/test-data/overlap.curve | 200 --
tests/test-data/paired-broken.fq.1 | 12 +
tests/test-data/paired-broken.fq.2 | 9 +
tests/test-data/paired-broken2.fq.1 | 8 +
tests/test-data/paired-broken2.fq.2 | 13 +
tests/test-data/paired-broken3.fq.1 | 12 +
tests/test-data/paired-broken3.fq.2 | 9 +
.../{paired-mixed.fq => paired-mixed-2.fq} | 6 +-
tests/test-data/paired-mixed-broken.fq | 4 +
tests/test-data/paired-mixed.fq | 4 +-
tests/test-data/paired-mixed.fq.pe | 4 +-
tests/test-data/random-20-a.fq | 4 +-
tests/test-data/simple_1.fa | 6 -
tests/test-data/simple_2.fa | 8 -
tests/test-data/simple_3.fa | 4 -
tests/test-data/test-abund-read-2.fq | 4 +-
...red-mixed.fq.pe => test-abund-read-2.paired.fq} | 52 +-
...ed-mixed.fq.pe => test-abund-read-2.paired2.fq} | 52 +-
tests/test-data/test-abund-read-paired.fa | 4 +-
...aired-mixed.fq.pe => test-abund-read-paired.fq} | 4 +-
tests/test-data/test-colors.fa | 8 -
tests/test-data/test-est.fa | 2 -
tests/test-data/test-graph3.fa | 8 -
tests/test-data/test-graph4.fa | 12 -
tests/test-data/test-graph6.fa | 464 ----
tests/test-data/test-reads.fq.gz | Bin 0 -> 763372 bytes
tests/test-data/truncated.fq | 5 +
tests/test_c_wrapper.py | 48 -
tests/test_counting_hash.py | 144 +-
tests/test_counting_single.py | 13 +-
tests/test_filter.py | 2 +-
tests/test_functions.py | 233 +-
tests/test_graph.py | 24 +-
tests/test_hashbits.py | 11 +-
tests/test_hashbits_obj.py | 13 +-
tests/test_hll.py | 250 ++
tests/test_labelhash.py | 11 +-
tests/test_lump.py | 2 +-
tests/test_read_aligner.py | 10 +-
tests/test_read_parsers.py | 78 +-
tests/test_sandbox_scripts.py | 169 +-
tests/test_script_arguments.py | 26 +-
tests/test_scripts.py | 1524 +++++++++--
tests/test_subset_graph.py | 30 +-
tests/test_threaded_sequence_processor.py | 6 +-
tests/test_version.py | 2 +-
third-party/.gitignore | 6 +
third-party/smhasher/MurmurHash3.cc | 147 ++
third-party/smhasher/MurmurHash3.h | 34 +
versioneer.py | 331 ++-
246 files changed, 9760 insertions(+), 5892 deletions(-)
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