[med-svn] [khmer] branch daube/libkhmerdev updated (06ade8d -> b391852)
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Jul 9 00:50:46 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch daube/libkhmerdev
in repository khmer.
from 06ade8d Update changelog with UNRELEASED 2.0-rc1
new f18516c s/ged-lab/dib-lab/g in disable_google_analytics
adds b80fa2e Revert "Merge tag 'upstream/2.0-rc1'"
adds 46f0f9d Revert "Import of RELEASE CANDIDATE v2.0-rc1: Not for upload"
adds f38372a Imported Upstream version 2.0rc1+dfsg
adds 4098cbc Merge tag 'upstream/2.0rc1+dfsg'
adds ebb982c version bump
new b391852 Merge branch 'master' into libkhmerdev
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 +-
debian/changelog | 13 +-
debian/control | 2 +-
debian/patches/disable_google_analytics | 2 +-
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 +-
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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/{_khmer.cc => _khmermodule.cc} | 3782 +-
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 +-
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lib/hashbits.cc | 35 +-
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lib/hashtable.hh | 26 +-
lib/hllcounter.cc | 13 +-
lib/hllcounter.hh | 2 +-
lib/ht-diff.cc | 4 +-
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lib/khmer_exception.hh | 4 +-
lib/kmer_hash.cc | 2 +-
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lib/labelhash.cc | 250 +-
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lib/magic | 11 -
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lib/subset.cc | 37 +-
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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 +-
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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 +-
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sandbox/unique-kmers.py | 45 +-
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scripts/abundance-dist-single.py | 67 +-
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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.py => test_hashbits_obj.py} | 458 +-
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 +-
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tests/test_subset_graph.py | 211 +-
tests/test_threaded_sequence_processor.py | 13 +-
tests/test_version.py | 19 +-
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