[med-svn] [khmer] 02/03: Merge tag 'upstream/2.1.1+dfsg' into experimental-2.1
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jun 23 13:36:27 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 6683f812f72d1c2229dd26424d73e3163a66c1f0
Merge: 2e45ec4 a119d2c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Fri Jun 23 05:47:57 2017 -0700
Merge tag 'upstream/2.1.1+dfsg' into experimental-2.1
Upstream version 2.1.1+dfsg
.github/CONTRIBUTING.md | 2 -
.gitignore | 1 +
.mailmap | 7 +
.travis.yml | 7 +-
.ycm_extra_conf.py | 105 -
CHANGELOG.md | 18 +-
MANIFEST.in | 5 +-
Makefile | 75 +-
README.rst | 123 +-
author-skips.txt | 15 +
authors.csv | 68 +
data/16s+23s.fa | 800 -
data/16s.fa | 714 -
data/1m-bigpart.fa | 44872 --------
data/23s.fa | 86 -
data/MSB2-part.group1.fa | 100806 -----------------
data/MSB2-part.group10.fa | 101128 -----------------
data/MSB2-part.group31.fa | 103446 ------------------
data/high-sodd.fa | 384 -
data/mda-test.fa | 28 -
data/primers.fa | 4 -
doc/conf.py | 18 +-
doc/contributors.rst | 37 +-
doc/dev/a-quick-guide-to-testing.rst | 42 +-
doc/dev/binary-file-formats.rst | 14 +-
doc/dev/codebase-guide.rst | 7 +-
doc/dev/crazy-ideas.rst | 47 -
doc/dev/details.rst | 42 -
doc/dev/development.rst | 33 +-
doc/dev/for-khmer-developers.rst | 33 +-
doc/dev/getting-started.rst | 379 +-
...and-review.rst => guidelines-continued-dev.rst} | 170 +-
doc/dev/index.rst | 16 +-
doc/dev/release.rst | 107 +-
doc/index.rst | 31 +-
doc/introduction.rst | 101 +-
doc/release-notes/release-1.2.md | 64 +-
doc/release-notes/release-1.2.rst | 25 +-
doc/release-notes/release-1.4.md | 10 +-
doc/release-notes/release-1.4.rst | 12 +-
doc/release-notes/release-2.0.md | 4 +-
doc/release-notes/release-2.0.rst | 4 +-
doc/release-notes/release-2.1.md | 47 +
doc/release-notes/release-2.1.rst | 78 +
doc/requirements.txt | 1 +
doc/user/api-examples.rst | 58 +-
doc/user/choosing-table-sizes.rst | 53 +-
doc/user/install.rst | 29 +-
doc/user/known-issues.rst | 23 +-
doc/whats-new-2.0.rst | 197 -
examples/c++-api/.gitignore | 4 +-
examples/c++-api/Makefile | 18 +-
examples/c++-api/bloom.cc | 38 +
examples/c++-api/consume.cc | 39 +
.../c++-api/{count-demo.cc => exact-counting.cc} | 23 +-
examples/c++-api/reads.fastq | 532 +
examples/python-api/bloom.py | 26 +
examples/python-api/consume.py | 20 +
examples/python-api/exact-counting.py | 39 +
examples/stamps/do.sh | 8 +-
ez_setup.py | 332 -
khmer/__init__.py | 13 +
khmer/_khmer.cc | 2 +-
khmer/_version.py | 118 +-
khmer/khmer_args.py | 38 +-
lib/assembler.cc | 64 +-
lib/assembler.hh | 16 +-
lib/hashtable.cc | 46 -
lib/hashtable.hh | 130 +-
lib/khmer.hh | 1 -
lib/kmer_filters.cc | 2 +-
lib/kmer_filters.hh | 2 +-
lib/magic | 1 -
lib/read_parsers.cc | 5 +-
lib/read_parsers.hh | 8 +-
lib/traversal.cc | 69 +-
lib/traversal.hh | 42 +-
papers/paper-v2.1.md | 121 +
sandbox/memusg | 46 -
scripts/abundance-dist-single.py | 18 +-
scripts/annotate-partitions.py | 2 +-
scripts/do-partition.py | 10 +-
scripts/extract-paired-reads.py | 4 +-
scripts/extract-partitions.py | 8 +-
scripts/filter-abund-single.py | 6 +-
scripts/filter-abund.py | 6 +-
scripts/filter-stoptags.py | 4 +-
scripts/load-into-counting.py | 2 +-
scripts/make-initial-stoptags.py | 4 +-
scripts/merge-partitions.py | 2 +-
scripts/normalize-by-median.py | 15 +-
scripts/partition-graph.py | 8 +-
scripts/readstats.py | 1 -
scripts/trim-low-abund.py | 73 +-
scripts/unique-kmers.py | 8 +-
setup.py | 42 +-
sort-authors-list.py | 22 +-
tests/khmer_tst_utils.py | 5 +-
tests/test-data/goodversion-k12.ht | Bin 16 -> 28 bytes
tests/test-data/goodversion-k12.ht.gz | Bin 38 -> 56 bytes
tests/test-data/goodversion-k32.stoptags | Bin 1174 -> 1354 bytes
tests/test-data/valid-read-testing.fq | 36 +
tests/test_assembly.py | 20 +
tests/test_counttable.py | 19 +
tests/test_nibblestorage.py | 14 +-
tests/test_nodegraph.py | 29 +-
tests/test_read_parsers.py | 22 +-
tests/test_sandbox_scripts.py | 32 +-
tests/test_script_arguments.py | 32 +-
tests/test_scripts.py | 70 +-
tests/test_sequence_validation.py | 335 +
tests/test_tabletype.py | 4 +-
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 256905 -> 0 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 32348 -> 0 bytes
third-party/bzip2/sample1.ref | Bin 98696 -> 0 bytes
third-party/bzip2/sample2.bz2 | Bin 73732 -> 0 bytes
third-party/bzip2/sample2.ref | Bin 212340 -> 0 bytes
third-party/bzip2/sample3.bz2 | Bin 235 -> 0 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/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 8734 -> 0 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 | 525 +-
230 files changed, 3098 insertions(+), 498279 deletions(-)
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