[med-svn] [bedtools] 01/02: Merge tag 'v2.21.0' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 19 01:06:11 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/unstable
in repository bedtools.
commit 856a5fd43cbb9b4c694cdc1421426a7fb71ef0e7
Merge: 08063ad 4356ace
Author: Charles Plessy <plessy at debian.org>
Date: Fri Sep 19 10:03:30 2014 +0900
Merge tag 'v2.21.0' into debian/unstable
Makefile | 5 +-
RELEASE_HISTORY | 86 ++-
docs/_static/labibi.css | 9 -
docs/bedtools.swiss.png | Bin 0 -> 8133 bytes
docs/conf.py | 2 +-
docs/content/bedtools-suite.rst | 3 +-
docs/content/history.rst | 12 +
.../content/images/tool-glyphs/intersect-glyph.png | Bin 34437 -> 94521 bytes
docs/content/installation.rst | 48 +-
docs/content/overview.rst | 2 +-
docs/content/tools/coverage.rst | 9 +-
docs/content/tools/fisher.rst | 119 ++++
docs/content/tools/intersect.rst | 222 +++++-
docs/templates/page.html | 7 +-
docs/templates/sidebar-intro.html | 11 +-
genomes/human.hg38.genome | 455 ++++++++++++
src/bedtools.cpp | 3 +
src/fisher/Fisher.cpp | 112 +++
src/fisher/Fisher.h | 30 +
src/fisher/Makefile | 49 ++
src/fisher/fisherMain.cpp | 72 ++
src/fisher/kfunc.c | 253 +++++++
src/intersectFile/intersectFile.cpp | 14 +-
src/intersectFile/intersectFile.h | 6 +-
src/intersectFile/intersectMain.cpp | 18 +-
src/jaccard/Jaccard.cpp | 12 +-
src/jaccard/Jaccard.h | 2 +-
src/mapFile/mapFile.cpp | 6 +-
src/mapFile/mapFile.h | 4 +-
src/mapFile/mapMain.cpp | 3 +-
src/mergeFile/mergeFile.cpp | 2 +-
src/nekSandbox1/nekSandboxMain.cpp | 2 -
src/regressTest/RegressTest.h | 5 +-
src/sampleFile/SampleFile.h | 4 +-
src/slopBed/slopBed.cpp | 8 +-
src/subtractBed/subtractBed.cpp | 2 +-
.../BamTools/src/api/internal/io/HostInfo_p.cpp | 3 +
.../src/api/internal/io/TcpSocketEngine_unix_p.cpp | 4 +-
src/utils/BinTree/BinTree.cpp | 38 +-
src/utils/BinTree/BinTree.h | 11 +-
src/utils/Contexts/ContextBase.cpp | 99 ++-
src/utils/Contexts/ContextBase.h | 51 +-
src/utils/Contexts/ContextFisher.cpp | 115 ++++
src/utils/Contexts/ContextFisher.h | 26 +
src/utils/Contexts/ContextIntersect.cpp | 58 +-
src/utils/Contexts/ContextIntersect.h | 18 +-
src/utils/Contexts/ContextMap.cpp | 14 +
src/utils/Contexts/ContextMap.h | 2 +
src/utils/Contexts/Makefile | 7 +-
src/utils/Fasta/Fasta.cpp | 6 +-
.../FileRecordTools/FileReaders/BamFileReader.h | 2 -
.../FileReaders/BufferedStreamMgr.cpp | 4 +-
.../FileReaders/BufferedStreamMgr.h | 7 +-
.../FileRecordTools/FileReaders/FileReader.cpp | 2 +-
src/utils/FileRecordTools/FileReaders/FileReader.h | 8 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 4 +-
src/utils/FileRecordTools/FileReaders/Makefile | 6 +-
.../FileReaders/{Makefile => Makefile~} | 0
.../FileReaders/SingleLineDelimTextFileReader.h | 2 -
.../FileReaders/SingleLineDelimTransferBuffer.cpp | 2 +
.../FileReaders/SingleLineDelimTransferBuffer.h | 2 -
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 16 +-
src/utils/FileRecordTools/FileRecordMergeMgr.h | 8 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 11 +-
src/utils/FileRecordTools/FileRecordMgr.h | 18 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 15 +-
src/utils/FileRecordTools/Records/BamRecord.h | 10 +-
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 38 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 19 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 1 +
src/utils/FileRecordTools/Records/Makefile | 14 +-
src/utils/FileRecordTools/Records/Record.cpp | 34 +-
src/utils/FileRecordTools/Records/Record.h | 19 +-
src/utils/FileRecordTools/Records/RecordKeyList.h | 13 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 88 +++
.../FileRecordTools/Records/RecordKeyVector.h | 62 ++
src/utils/FileRecordTools/Records/RecordList.cpp | 202 ++++++
src/utils/FileRecordTools/Records/RecordList.h | 117 ++++
src/utils/FileRecordTools/Records/StrandQueue.h | 6 +-
src/utils/FileRecordTools/Records/VcfRecord.cpp | 5 +-
src/utils/GenomeFile/NewGenomeFile.cpp | 17 +-
src/utils/GenomeFile/NewGenomeFile.h | 2 +-
src/utils/KeyListOps/KeyListOps.cpp | 2 +-
src/utils/KeyListOps/KeyListOps.h | 4 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 6 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 16 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 221 +++---
src/utils/NewChromsweep/NewChromsweep.h | 63 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 17 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 1 +
src/utils/fileType/FileRecordTypeChecker.h | 6 +-
src/utils/general/CommonHelp.cpp | 17 +
src/utils/general/CommonHelp.h | 19 +
src/utils/general/CompressionTools.h | 2 -
src/utils/general/FreeList.h | 4 +-
src/utils/general/Makefile | 7 +-
src/utils/general/ParseTools.h | 4 +-
src/utils/general/PushBackStreamBuf.h | 6 +-
src/utils/general/QuickString.cpp | 5 +
src/utils/general/QuickString.h | 4 +-
src/utils/general/Tokenizer.h | 4 +-
src/utils/version/version_release.txt | 6 +-
test/general/test-general.sh | 2 +-
test/intersect/multi_intersect/d1.bed | 9 +
test/intersect/multi_intersect/d2.bed | 6 +
test/intersect/multi_intersect/d3.bed | 3 +
test/intersect/multi_intersect/d4.bed | 9 +
test/intersect/multi_intersect/d5.bed | 6 +
test/intersect/multi_intersect/d6.bed | 3 +
test/intersect/multi_intersect/d7.bed | 10 +
test/intersect/multi_intersect/d8.bed | 7 +
test/intersect/multi_intersect/d9.bed | 4 +
test/intersect/multi_intersect/g.bed | 3 +
test/intersect/multi_intersect/query.bed | 12 +
test/intersect/multi_intersect/query2.bed | 13 +
test/intersect/multi_intersect/query3.bed | 13 +
.../multi_intersect/test-multi_intersect.sh | 404 +++++++++++
test/intersect/new_test-intersect.sh~ | 766 +++++++++++++++++++++
test/intersect/performanceTest.sh | 2 +-
test/intersect/test-intersect.sh | 7 +-
test/merge/test-merge.sh | 69 ++
test/slop/test-slop.sh | 8 +-
124 files changed, 4140 insertions(+), 468 deletions(-)
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