[med-svn] [khmer] branch master updated (b04fcb4 -> de9a334)
Kevin Murray
daube-guest at moszumanska.debian.org
Wed Jul 8 11:43:24 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository khmer.
from b04fcb4 Merge tag 'upstream/1.4+dfsg'
new aafc163 Import of RELEASE CANDIDATE v2.0-rc1: Not for upload
new de9a334 Merge tag 'upstream/2.0-rc1'
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 3 +
CITATION | 2 +-
ChangeLog | 354 +-
Doxyfile.in | 2 +-
Makefile | 34 +-
README.rst | 15 +-
doc/conf.py | 2 +-
doc/dev/binary-file-formats.rst | 115 +
doc/dev/development.rst | 6 +-
doc/dev/for-khmer-developers.rst | 4 +-
doc/dev/getting-started.rst | 29 +-
doc/dev/hackathon.rst | 12 +-
doc/dev/index.rst | 1 +
doc/dev/release.rst | 20 +-
doc/dev/scripts-and-sandbox.rst | 2 +-
doc/index.rst | 5 +-
doc/release-notes/release-1.0.1.md | 12 +-
doc/release-notes/release-1.0.1.rst | 14 +-
doc/release-notes/release-1.0.md | 12 +-
doc/release-notes/release-1.0.rst | 16 +-
doc/release-notes/release-1.1.md | 14 +-
doc/release-notes/release-1.1.rst | 14 +-
doc/release-notes/release-1.2.md | 14 +-
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doc/release-notes/release-1.3.md | 2 +-
doc/release-notes/release-1.3.rst | 2 +-
doc/release-notes/release-1.4.md | 4 +-
doc/release-notes/release-1.4.rst | 4 +-
doc/roadmap.rst | 2 +-
doc/run-corn-50m.sh | 4 +-
doc/user/choosing-table-sizes.rst | 74 +-
doc/user/examples.rst | 4 +-
doc/user/getting-help.rst | 2 +-
doc/user/guide.rst | 2 +-
doc/user/known-issues.rst | 14 +-
doc/user/scripts.rst | 12 +-
doc/whats-new-2.0.rst | 29 +
examples/stamps/do.sh | 4 +-
jenkins-build.sh | 2 +-
khmer/__init__.py | 120 +-
khmer/{_khmermodule.cc => _khmer.cc} | 3792 +-
khmer/_version.py | 11 +-
khmer/kfile.py | 72 +-
khmer/khmer_args.py | 175 +-
khmer/thread_utils.py | 66 +-
khmer/utils.py | 46 +-
lib/.check_openmp.cc | 2 +-
lib/Makefile | 2 +-
lib/counting.cc | 70 +-
lib/counting.hh | 2 +-
lib/get_version.py | 3 +-
lib/graphtest.cc | 4 +-
lib/hashbits.cc | 35 +-
lib/hashbits.hh | 11 +-
lib/hashtable.cc | 119 +-
lib/hashtable.hh | 26 +-
lib/hllcounter.cc | 13 +-
lib/hllcounter.hh | 2 +-
lib/ht-diff.cc | 4 +-
lib/khmer.hh | 12 +-
lib/khmer_exception.hh | 4 +-
lib/kmer_hash.cc | 2 +-
lib/kmer_hash.hh | 2 +-
lib/labelhash.cc | 250 +-
lib/labelhash.hh | 33 +-
lib/magic | 11 +
lib/perf_metrics.cc | 4 +-
lib/perf_metrics.hh | 4 +-
lib/primes.hh | 4 +-
lib/read_aligner.cc | 4 +-
lib/read_aligner.hh | 4 +-
lib/read_parsers.cc | 4 +-
lib/read_parsers.hh | 4 +-
lib/subset.cc | 37 +-
lib/subset.hh | 4 +-
lib/test-Colors.cc | 4 +-
lib/test-HashTables.cc | 4 +-
lib/test-Parser.cc | 4 +-
lib/test-compile.cc | 2 +-
lib/trace_logger.cc | 4 +-
lib/trace_logger.hh | 4 +-
oxli/__init__.py | 55 +
oxli/build_graph.py | 103 +
oxli/functions.py | 103 +
sandbox/README.rst | 230 +-
sandbox/abundance-hist-by-position.py | 16 +-
sandbox/assembly-diff-2.py | 19 +-
sandbox/assembly-diff.py | 16 +-
sandbox/assemstats3.py | 28 +-
sandbox/bloom-count-intersection.py | 25 +-
sandbox/bloom-count.py | 15 +-
sandbox/build-sparse-graph.py | 15 +-
sandbox/calc-best-assembly.py | 25 +-
sandbox/calc-error-profile.py | 40 +-
sandbox/calc-median-distribution.py | 12 +-
sandbox/collect-reads.py | 44 +-
sandbox/collect-variants.py | 49 +-
sandbox/correct-errors.py | 41 +-
sandbox/estimate_optimal_hash.py | 109 +
sandbox/extract-single-partition.py | 9 +-
sandbox/fasta-to-abundance-hist.py | 15 +-
sandbox/filter-below-abund.py | 19 +-
sandbox/filter-median-and-pct.py | 21 +-
sandbox/filter-median.py | 17 +-
sandbox/find-high-abund-kmers.py | 51 +-
sandbox/graph-size.py | 31 +-
sandbox/hi-lo-abundance-by-position.py | 13 +-
sandbox/make-coverage.py | 19 +-
sandbox/multi-rename.py | 9 +-
sandbox/normalize-by-median-pct.py | 82 +-
sandbox/optimal_args_hashbits.py | 97 +
sandbox/print-stoptags.py | 8 +-
sandbox/print-tagset.py | 11 +-
sandbox/renumber-partitions.py | 11 +-
sandbox/saturate-by-median.py | 58 +-
sandbox/shuffle-reverse-rotary.py | 13 +-
sandbox/slice-reads-by-coverage.py | 19 +-
sandbox/split-fasta.py | 11 +-
sandbox/split-sequences-by-length.py | 11 +-
sandbox/stoptag-abundance-hist.py | 11 +-
sandbox/stoptags-by-position.py | 11 +-
sandbox/strip-partition.py | 9 +-
sandbox/subset-report.py | 23 +-
sandbox/sweep-files.py | 51 +-
sandbox/sweep-out-reads-with-contigs.py | 13 +-
sandbox/sweep-reads.py | 121 +-
sandbox/sweep-reads2.py | 43 +-
sandbox/sweep-reads3.py | 43 +-
sandbox/unique-kmers.py | 45 +-
sandbox/write-trimmomatic.py | 11 +-
scripts/abundance-dist-single.py | 67 +-
scripts/abundance-dist.py | 25 +-
scripts/annotate-partitions.py | 17 +-
scripts/count-median.py | 18 +-
scripts/count-overlap.py | 22 +-
scripts/do-partition.py | 94 +-
scripts/extract-long-sequences.py | 7 +-
scripts/extract-paired-reads.py | 113 +-
scripts/extract-partitions.py | 72 +-
scripts/fastq-to-fasta.py | 19 +-
scripts/filter-abund-single.py | 49 +-
scripts/filter-abund.py | 33 +-
scripts/filter-stoptags.py | 13 +-
scripts/find-knots.py | 74 +-
scripts/interleave-reads.py | 41 +-
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scripts/load-into-counting.py | 50 +-
scripts/make-initial-stoptags.py | 23 +-
scripts/merge-partitions.py | 17 +-
scripts/normalize-by-median.py | 396 +-
scripts/partition-graph.py | 64 +-
scripts/readstats.py | 25 +-
scripts/sample-reads-randomly.py | 42 +-
scripts/split-paired-reads.py | 60 +-
scripts/trim-low-abund.py | 94 +-
setup.cfg | 4 +-
setup.py | 22 +-
tests/__init__.py | 4 +-
tests/khmer_tst_utils.py | 32 +-
tests/test-data/badversion-k32.tagset | Bin 16 -> 20 bytes
tests/test-data/dn-test-all-paired-all-keep.fa | 16 +
tests/test-data/dn-test-none-paired.fa | 8 +
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tests/test-data/normC20k20.ct | Bin 40140 -> 40144 bytes
tests/test-data/paired-slash1.fq | 32 +
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tests/test-data/paired-slash1.fq.2 | 16 +
tests/test-data/paired_one.base.dif.fa | 5 +
tests/test-data/test-filter-abund-Ns.fq | 16 +
tests/test_counting_hash.py | 680 +-
tests/test_counting_single.py | 90 +-
tests/test_filter.py | 16 +-
tests/test_functions.py | 76 +-
tests/test_graph.py | 46 +-
tests/test_hashbits.py | 327 +-
tests/test_hashbits_obj.py | 563 -
tests/test_hll.py | 76 +-
tests/test_labelhash.py | 764 +-
tests/test_lump.py | 31 +-
tests/test_normalize_by_median.py | 627 +
tests/test_oxli_functions.py | 60 +
tests/test_read_aligner.py | 18 +-
tests/test_read_parsers.py | 36 +-
tests/test_sandbox_scripts.py | 70 +-
tests/test_script_arguments.py | 218 +-
tests/test_scripts.py | 1384 +-
tests/test_subset_graph.py | 211 +-
tests/test_threaded_sequence_processor.py | 13 +-
tests/test_version.py | 19 +-
third-party/bzip2/.gitignore | 2 +
third-party/bzip2/CHANGES | 327 +
third-party/bzip2/LICENSE | 42 +
third-party/bzip2/Makefile | 217 +
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third-party/bzip2/README | 215 +
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third-party/zlib/inftrees.c | 306 +
third-party/zlib/inftrees.h | 62 +
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third-party/zlib/old/README | 3 +
third-party/zlib/old/descrip.mms | 48 +
third-party/zlib/old/os2/Makefile.os2 | 136 +
third-party/zlib/old/os2/zlib.def | 51 +
third-party/zlib/old/visual-basic.txt | 160 +
third-party/zlib/qnx/package.qpg | 141 +
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/watcom/watcom_f.mak | 43 +
third-party/zlib/watcom/watcom_l.mak | 43 +
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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 | 1 +
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