[med-svn] [khmer] 02/02: Merge tag 'upstream/2.0-rc1'
Kevin Murray
daube-guest at moszumanska.debian.org
Wed Jul 8 11:43:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository khmer.
commit de9a33473ab505130cd6fc828246b8ba63f03ea3
Merge: b04fcb4 aafc163
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Wed Jul 8 21:42:05 2015 +1000
Merge tag 'upstream/2.0-rc1'
Upstream version 2.0-rc1
.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 +-
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doc/dev/hackathon.rst | 12 +-
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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 +-
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sandbox/estimate_optimal_hash.py | 109 +
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sandbox/filter-below-abund.py | 19 +-
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sandbox/split-fasta.py | 11 +-
sandbox/split-sequences-by-length.py | 11 +-
sandbox/stoptag-abundance-hist.py | 11 +-
sandbox/stoptags-by-position.py | 11 +-
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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_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 +-
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third-party/zlib/inffast.h | 11 +
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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/msdos/Makefile.bor | 115 +
third-party/zlib/msdos/Makefile.dj2 | 104 +
third-party/zlib/msdos/Makefile.emx | 69 +
third-party/zlib/msdos/Makefile.msc | 112 +
third-party/zlib/msdos/Makefile.tc | 100 +
third-party/zlib/nintendods/README | 5 +
third-party/zlib/old/Makefile.emx | 69 +
third-party/zlib/old/Makefile.riscos | 151 +
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 +
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 | 1 +
482 files changed, 197484 insertions(+), 6084 deletions(-)
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