[med-svn] [khmer] 02/06: Merge tag 'upstream/2.0_pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 20 13:11:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch experimental-2.1
in repository khmer.
commit dbb76ccf75b96edb4e828bdcae27fd9c73d0484f
Merge: 4b3105d 021bb43
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Mon Feb 20 01:45:07 2017 -0800
Merge tag 'upstream/2.0_pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12'
Upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
.dictionary | 155 +
CONTRIBUTING.md => .github/CONTRIBUTING.md | 18 +-
.github/PULL_REQUEST_TEMPLATE.md | 16 +
.gitignore | 4 +-
.mailmap | 3 +-
.travis.yml | 88 +
.ycm_extra_conf.py | 105 +
CHANGELOG.md | 65 +
CITATION | 12 +-
IDEAS | 18 -
Makefile | 182 +-
README.rst | 68 +-
TODO | 80 -
ci_scripts/install.sh | 31 +
doc/conf.py | 13 +-
doc/contributors.rst | 14 +-
doc/dev/a-quick-guide-to-testing.rst | 14 +-
doc/dev/codebase-guide.rst | 16 +-
doc/dev/coding-guidelines-and-review.rst | 64 +-
doc/dev/development.rst | 62 +-
doc/dev/getting-started.rst | 52 +-
doc/dev/python-api.rst | 152 +
doc/dev/release.rst | 40 +-
doc/dev/scripts-and-sandbox.rst | 47 +-
doc/index.rst | 22 +-
doc/introduction.rst | 92 +-
doc/requirements.txt | 4 +-
doc/roadmap.rst | 16 +-
doc/user/api-examples.rst | 94 +
doc/user/blog-posts.rst | 22 +-
doc/user/guide.rst | 16 +-
doc/user/index.rst | 16 +-
doc/user/install.rst | 14 -
doc/whats-new-2.0.rst | 12 +-
examples/README.txt | 5 -
examples/c++-api/.gitignore | 1 +
examples/c++-api/Makefile | 10 +
examples/c++-api/count-demo.cc | 41 +
ez_setup.py | 332 +
khmer/__init__.py | 159 +-
khmer/_cpy_counttable.hh | 128 +
khmer/_cpy_hashgraph.hh | 1587 +
khmer/_cpy_nodetable.hh | 131 +
khmer/_cpy_smallcountgraph.hh | 181 +
khmer/_cpy_smallcounttable.hh | 127 +
khmer/_khmer.cc | 6098 +-
khmer/_version.py | 430 +-
khmer/kfile.py | 38 +-
khmer/khmer_args.py | 340 +-
khmer/khmer_logger.py | 13 +-
khmer/thread_utils.py | 68 +-
khmer/{khmer_logger.py => trimming.py} | 66 +-
khmer/utils.py | 115 +-
ChangeLog => legacy/ChangeLog | 662 +-
jenkins-build.sh => legacy/jenkins-build.sh | 12 +-
lib/.gitignore | 1 +
lib/Makefile | 18 +-
lib/{test-compile.cc => alphabets.cc} | 21 +-
lib/{test-compile.cc => alphabets.hh} | 22 +-
lib/assembler.cc | 523 +
lib/assembler.hh | 177 +
lib/counting.cc | 1041 -
lib/counting.hh | 348 -
lib/get_version.py | 52 -
lib/hashbits.cc | 215 -
lib/hashbits.hh | 215 -
lib/{hashtable.cc => hashgraph.cc} | 760 +-
lib/hashgraph.hh | 298 +
lib/hashtable.cc | 1200 +-
lib/hashtable.hh | 432 +-
lib/hllcounter.cc | 39 +-
lib/hllcounter.hh | 33 +-
lib/khmer.hh | 23 +-
lib/kmer_filters.cc | 159 +
lib/{test-Colors.cc => kmer_filters.hh} | 42 +-
lib/kmer_hash.cc | 47 +-
lib/kmer_hash.hh | 98 +-
lib/labelhash.cc | 198 +-
lib/labelhash.hh | 110 +-
lib/magic | 62 +-
lib/oxli.pc.in | 4 +-
lib/read_aligner.cc | 24 +-
lib/read_aligner.hh | 8 +-
lib/read_parsers.cc | 406 +-
lib/read_parsers.hh | 185 +-
lib/storage.cc | 916 +
lib/storage.hh | 651 +
lib/subset.cc | 339 +-
lib/subset.hh | 31 +-
lib/test-Colors.cc | 2 +-
lib/test-compile.cc | 4 +-
lib/traversal.cc | 302 +-
lib/traversal.hh | 259 +-
oxli/__init__.py | 15 +-
oxli/build_graph.py | 14 +-
oxli/functions.py | 21 +-
oxli/partition.py | 49 +
pylintrc | 384 +
pytest.ini | 4 +
sandbox/Makefile.read_aligner_training | 26 +-
sandbox/README.rst | 16 +-
sandbox/abundance-hist-by-position.py | 70 -
sandbox/assemble-and-track.py | 139 +
sandbox/assemble-on-the-go.py | 118 +
sandbox/assembly-diff.py | 4 +-
sandbox/assemstats3.py | 3 +-
sandbox/bloom-count.py | 3 +
sandbox/collect-reads.py | 3 +-
sandbox/collect-variants.py | 3 +-
sandbox/count-kmers-single.py | 5 +-
sandbox/count-kmers.py | 3 +-
sandbox/extract-compact-dbg.py | 230 +
sandbox/extract-unassembled-reads-2.py | 72 +
sandbox/extract-unassembled-reads.py | 86 +
sandbox/find-high-abund-kmers.py | 107 -
sandbox/graph-size.py | 2 +-
sandbox/link-compact-dbg.py | 198 +
sandbox/memusg | 46 +
sandbox/optimal_args_hashbits.py | 5 +-
sandbox/readaligner_pairhmm_train.py | 14 +-
sandbox/reassemble-contigs.py | 51 +
sandbox/saturate-by-median.py | 3 +-
sandbox/stoptag-abundance-hist.py | 2 +
sandbox/streaming-assembly-simple.py | 145 +
sandbox/sweep-out-reads-with-contigs.py | 2 +-
sandbox/sweep-reads2.py | 63 +-
sandbox/sweep-reads3.py | 5 +-
scripts/abundance-dist-single.py | 69 +-
scripts/abundance-dist.py | 60 +-
scripts/annotate-partitions.py | 11 +-
scripts/count-median.py | 16 +-
scripts/do-partition.py | 46 +-
scripts/extract-long-sequences.py | 11 +-
scripts/extract-paired-reads.py | 28 +-
scripts/extract-partitions.py | 300 +-
scripts/fastq-to-fasta.py | 20 +-
scripts/filter-abund-single.py | 103 +-
scripts/filter-abund.py | 94 +-
scripts/filter-stoptags.py | 15 +-
scripts/find-knots.py | 13 +-
scripts/interleave-reads.py | 46 +-
scripts/load-graph.py | 6 +-
scripts/load-into-counting.py | 61 +-
scripts/make-initial-stoptags.py | 10 +-
scripts/merge-partitions.py | 13 +-
scripts/normalize-by-median.py | 50 +-
scripts/partition-graph.py | 48 +-
scripts/readstats.py | 25 +-
scripts/sample-reads-randomly.py | 38 +-
scripts/split-paired-reads.py | 36 +-
scripts/trim-low-abund.py | 477 +-
scripts/unique-kmers.py | 27 +-
setup.cfg | 24 +-
setup.py | 46 +-
tests/__init__.py | 1 +
tests/khmer_tst_utils.py | 108 +-
tests/test-data/README.rst | 10 +
tests/test-data/paired-mixed-witherror.fa.pe | 12 +
tests/test-data/paired.malformat.fq | 24 +
tests/test-data/paired.malformat.fq.2 | 12 +
tests/test-data/simple-genome-reads.fa | 2000 +
tests/test-data/simple-genome.fa | 2 +
tests/test-data/single-read.fa | 2 +
tests/test-data/unclean-reads.fastq | 8 +
tests/test_assembly.py | 886 +
tests/test_countgraph.py | 357 +-
tests/test_counting_single.py | 60 +-
.../test_counttable.py | 50 +-
.../test_cpython_hierarchy.py | 59 +-
tests/test_filter.py | 91 -
tests/test_filter_abund.py | 432 +
tests/test_functions.py | 280 +-
tests/test_graph.py | 32 +-
tests/test_hashset.py | 169 +
tests/test_hll.py | 73 +-
tests/test_labelhash.py | 78 +-
tests/test_lump.py | 31 +-
tests/test_nibblestorage.py | 129 +
tests/test_nodegraph.py | 462 +-
tests/test_normalize_by_median.py | 254 +-
tests/test_oxli_functions.py | 9 +-
tests/test_read_aligner.py | 127 +-
tests/test_read_handling.py | 789 +
tests/test_read_parsers.py | 136 +-
tests/test_sandbox_scripts.py | 100 +-
tests/test_script_arguments.py | 235 +-
tests/test_script_output.py | 184 +
tests/test_scripts.py | 1581 +-
tests/test_streaming_io.py | 92 +-
tests/test_subset_graph.py | 143 +-
tests/test_tabletype.py | 446 +
tests/test_threaded_sequence_processor.py | 47 +-
tests/test_version.py | 11 +-
third-party/bzip2/.gitignore | 2 +
third-party/bzip2/CHANGES | 327 +
third-party/bzip2/LICENSE | 42 +
third-party/bzip2/Makefile | 217 +
third-party/bzip2/Makefile-libbz2_so | 59 +
third-party/bzip2/README | 215 +
third-party/bzip2/README.COMPILATION.PROBLEMS | 58 +
third-party/bzip2/README.XML.STUFF | 45 +
third-party/bzip2/blocksort.c | 1094 +
third-party/bzip2/bz-common.xsl | 39 +
third-party/bzip2/bz-fo.xsl | 276 +
third-party/bzip2/bz-html.xsl | 20 +
third-party/bzip2/bzdiff | 76 +
third-party/bzip2/bzdiff.1 | 47 +
third-party/bzip2/bzgrep | 75 +
third-party/bzip2/bzgrep.1 | 56 +
third-party/bzip2/bzip.css | 74 +
third-party/bzip2/bzip2.1 | 454 +
third-party/bzip2/bzip2.1.preformatted | 399 +
third-party/bzip2/bzip2.c | 2034 +
third-party/bzip2/bzip2.txt | 391 +
third-party/bzip2/bzip2recover.c | 514 +
third-party/bzip2/bzlib.c | 1572 +
third-party/bzip2/bzlib.h | 282 +
third-party/bzip2/bzlib_private.h | 509 +
third-party/bzip2/bzmore | 61 +
third-party/bzip2/bzmore.1 | 152 +
third-party/bzip2/compress.c | 672 +
third-party/bzip2/crctable.c | 104 +
third-party/bzip2/decompress.c | 646 +
third-party/bzip2/dlltest.c | 175 +
third-party/bzip2/dlltest.dsp | 93 +
third-party/bzip2/entities.xml | 9 +
third-party/bzip2/format.pl | 68 +
third-party/bzip2/huffman.c | 205 +
third-party/bzip2/libbz2.def | 27 +
third-party/bzip2/libbz2.dsp | 130 +
third-party/bzip2/makefile.msc | 63 +
third-party/bzip2/manual.html | 2540 +
third-party/bzip2/manual.pdf | Bin 0 -> 256905 bytes
third-party/bzip2/manual.ps | 72843 +++++++++++++++++++
third-party/bzip2/manual.xml | 2964 +
third-party/bzip2/mk251.c | 31 +
third-party/bzip2/randtable.c | 84 +
third-party/bzip2/sample1.bz2 | Bin 0 -> 32348 bytes
third-party/bzip2/sample1.ref | Bin 0 -> 98696 bytes
third-party/bzip2/sample2.bz2 | Bin 0 -> 73732 bytes
third-party/bzip2/sample2.ref | Bin 0 -> 212340 bytes
third-party/bzip2/sample3.bz2 | Bin 0 -> 235 bytes
third-party/bzip2/sample3.ref | 30007 ++++++++
third-party/bzip2/spewG.c | 54 +
third-party/bzip2/unzcrash.c | 141 +
third-party/bzip2/words0 | 9 +
third-party/bzip2/words1 | 4 +
third-party/bzip2/words2 | 5 +
third-party/bzip2/words3 | 30 +
third-party/bzip2/xmlproc.sh | 114 +
third-party/seqan/ChangeLog | 5 +
.../core/include/seqan/basic/debug_test_system.h | 2 +-
third-party/zlib/.gitignore | 5 +
third-party/zlib/CMakeLists.txt | 249 +
third-party/zlib/ChangeLog | 1472 +
third-party/zlib/FAQ | 368 +
third-party/zlib/INDEX | 68 +
third-party/zlib/Makefile.in | 288 +
third-party/zlib/Makefile.pic | 3 +
third-party/zlib/README | 115 +
third-party/zlib/adler32.c | 179 +
third-party/zlib/compress.c | 80 +
third-party/zlib/configure | 831 +
third-party/zlib/crc32.c | 425 +
third-party/zlib/crc32.h | 441 +
third-party/zlib/deflate.c | 1967 +
third-party/zlib/deflate.h | 346 +
third-party/zlib/doc/algorithm.txt | 209 +
third-party/zlib/doc/rfc1950.txt | 619 +
third-party/zlib/doc/rfc1951.txt | 955 +
third-party/zlib/doc/rfc1952.txt | 675 +
third-party/zlib/doc/txtvsbin.txt | 107 +
third-party/zlib/gzclose.c | 25 +
third-party/zlib/gzguts.h | 209 +
third-party/zlib/gzlib.c | 634 +
third-party/zlib/gzread.c | 594 +
third-party/zlib/gzwrite.c | 577 +
third-party/zlib/infback.c | 640 +
third-party/zlib/inffast.c | 340 +
third-party/zlib/inffast.h | 11 +
third-party/zlib/inffixed.h | 94 +
third-party/zlib/inflate.c | 1512 +
third-party/zlib/inflate.h | 122 +
third-party/zlib/inftrees.c | 306 +
third-party/zlib/inftrees.h | 62 +
third-party/zlib/make_vms.com | 867 +
third-party/zlib/test/example.c | 601 +
third-party/zlib/test/infcover.c | 671 +
third-party/zlib/test/minigzip.c | 651 +
third-party/zlib/treebuild.xml | 116 +
third-party/zlib/trees.c | 1226 +
third-party/zlib/trees.h | 128 +
third-party/zlib/uncompr.c | 59 +
third-party/zlib/win32/DLL_FAQ.txt | 397 +
third-party/zlib/win32/Makefile.bor | 110 +
third-party/zlib/win32/Makefile.gcc | 182 +
third-party/zlib/win32/Makefile.msc | 163 +
third-party/zlib/win32/README-WIN32.txt | 103 +
third-party/zlib/win32/VisualC.txt | 3 +
third-party/zlib/win32/zlib.def | 86 +
third-party/zlib/win32/zlib1.rc | 40 +
third-party/zlib/zconf.h.cmakein | 513 +
third-party/zlib/zconf.h.in | 511 +
third-party/zlib/zlib.3 | 151 +
third-party/zlib/zlib.3.pdf | Bin 0 -> 8734 bytes
third-party/zlib/zlib.h | 1768 +
third-party/zlib/zlib.map | 83 +
third-party/zlib/zlib.pc.cmakein | 13 +
third-party/zlib/zlib.pc.in | 13 +
third-party/zlib/zlib2ansi | 152 +
third-party/zlib/zutil.c | 324 +
third-party/zlib/zutil.h | 253 +
versioneer.py | 1668 +-
313 files changed, 167591 insertions(+), 12466 deletions(-)
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