[med-svn] [khmer] branch master updated (de9a334 -> ebb982c)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Jul 9 00:12:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from de9a334 Merge tag 'upstream/2.0-rc1'
new b80fa2e Revert "Merge tag 'upstream/2.0-rc1'"
new 46f0f9d Revert "Import of RELEASE CANDIDATE v2.0-rc1: Not for upload"
new f38372a Imported Upstream version 2.0rc1+dfsg
new 4098cbc Merge tag 'upstream/2.0rc1+dfsg'
new ebb982c version bump
The 5 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 | 6 +-
debian/control | 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/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/{_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/ht-diff.cc | 4 +-
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lib/magic | 11 -
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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 +-
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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 +-
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sandbox/sweep-reads2.py | 43 +-
sandbox/sweep-reads3.py | 43 +-
sandbox/unique-kmers.py | 45 +-
sandbox/write-trimmomatic.py | 11 +-
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tests/__init__.py | 4 +-
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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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