[med-svn] [bedtools] 01/02: Merge tag 'v2.20.1' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Sat May 24 13:36:48 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 7b6b2d6f0d1c5cd226f6baa6df52facb25ae76eb
Merge: 68dfd72 4122ba1
Author: Charles Plessy <plessy at debian.org>
Date: Sat May 24 21:48:23 2014 +0900
Merge tag 'v2.20.1' into debian/unstable
Makefile | 7 +-
README.md | 4 +-
RELEASE_HISTORY | 7 +
docs/conf.py | 6 +-
RELEASE_HISTORY => docs/content/history.rst | 482 +++++-----
docs/content/installation.rst | 2 +-
docs/content/tools/jaccard.rst | 3 +
docs/content/tools/map.rst | 2 -
docs/content/tools/merge.rst | 169 ++--
docs/content/tools/unionbedg.rst | 28 +-
docs/index.rst | 3 +-
src/intersectFile/intersectFile.cpp | 3 +-
src/jaccard/Jaccard.cpp | 94 ++
src/{mapFile/mapFile.h => jaccard/Jaccard.h} | 38 +-
src/jaccard/Makefile | 29 +-
src/jaccard/jaccard.cpp | 110 ---
src/jaccard/jaccard.h | 70 --
src/jaccard/jaccardMain.cpp | 240 +++--
src/mapFile/mapFile.h | 1 -
src/mapFile/mapMain.cpp | 18 +-
src/mergeBed/Makefile | 35 -
src/mergeBed/mergeBed.cpp | 359 -------
src/mergeBed/mergeBed.h | 72 --
src/mergeBed/mergeMain.cpp | 184 ----
src/mergeFile/Makefile | 46 +
src/mergeFile/mergeFile.cpp | 39 +
src/mergeFile/mergeFile.h | 37 +
src/mergeFile/mergeMain.cpp | 80 ++
src/nekSandbox1/nekSandboxMain.cpp | 6 +-
src/nucBed/nucBed.cpp | 6 +-
src/sampleFile/SampleFile.cpp | 2 +-
src/shuffleBed/shuffleBed.cpp | 51 +-
src/shuffleBed/shuffleBedMain.cpp | 2 -
src/slopBed/slopBed.cpp | 34 +-
src/utils/BamTools/src/api/BamAlignment.h | 2 +-
src/utils/BamTools/src/api/SamHeader.h | 4 +-
.../src/api/internal/io/TcpSocketEngine_p.h | 2 +-
.../src/api/internal/sam/SamHeaderValidator_p.h | 4 +-
src/utils/BinTree/BinTree.cpp | 9 +-
src/utils/BlockedIntervals/BlockedIntervals.cpp | 6 +-
src/utils/Contexts/ContextBase.cpp | 66 +-
src/utils/Contexts/ContextBase.h | 47 +-
src/utils/Contexts/ContextJaccard.cpp | 109 +++
src/utils/Contexts/ContextJaccard.h | 25 +
src/utils/Contexts/ContextMap.cpp | 10 -
src/utils/Contexts/ContextMap.h | 5 -
src/utils/Contexts/ContextMerge.cpp | 176 ++++
src/utils/Contexts/ContextMerge.h | 31 +
src/utils/Contexts/Makefile | 9 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 10 +
.../FileRecordTools/FileReaders/BamFileReader.h | 4 +-
.../FileReaders/BufferedStreamMgr.cpp | 30 +-
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 21 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 7 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 6 +-
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 217 +++++
src/utils/FileRecordTools/FileRecordMergeMgr.h | 58 ++
src/utils/FileRecordTools/FileRecordMgr.cpp | 186 +---
src/utils/FileRecordTools/FileRecordMgr.h | 79 +-
src/utils/FileRecordTools/Makefile | 10 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 209 ++--
src/utils/FileRecordTools/Records/BamRecord.h | 27 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 16 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 3 +
src/utils/FileRecordTools/Records/EmptyRecord.cpp | 34 +
src/utils/FileRecordTools/Records/EmptyRecord.h | 30 +
src/utils/FileRecordTools/Records/Makefile | 12 +-
src/utils/FileRecordTools/Records/Record.h | 5 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 24 +
src/utils/FileRecordTools/Records/RecordMgr.h | 1 +
src/utils/FileRecordTools/Records/StrandQueue.cpp | 131 +++
src/utils/FileRecordTools/Records/StrandQueue.h | 47 +
.../FileRecordTools/Records/recordsTar.tar.gz | Bin 54443 -> 0 bytes
src/utils/GenomeFile/NewGenomeFile.cpp | 12 +-
src/utils/KeyListOps/KeyListOps.cpp | 142 ++-
src/utils/KeyListOps/KeyListOps.h | 20 +
src/utils/KeyListOps/KeyListOpsMethods.cpp | 21 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 13 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 10 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 1 +
src/utils/bedFile/bedFile.cpp | 14 +
src/utils/bedFile/bedFile.h | 4 +
src/utils/fileType/FileRecordTypeChecker.cpp | 56 +-
src/utils/fileType/FileRecordTypeChecker.h | 19 +-
src/utils/fileType/fileType.cpp | 2 +-
src/utils/general/DualQueue.h | 124 ---
src/utils/general/Makefile | 6 +-
src/utils/general/ParseTools.cpp | 34 +-
src/utils/general/ParseTools.h | 4 +-
src/utils/general/QuickString.h | 1 +
src/utils/general/Tokenizer.cpp | 102 ++
src/utils/general/Tokenizer.h | 57 ++
src/utils/version/version_release.txt | 6 +-
test/general/test-general.sh | 204 +++-
test/intersect/dosLineCharWithExtraTab_b.bed | 4 +
test/intersect/dosLineChar_a.bed | 3 +
test/intersect/headerOnly.vcf | 121 +++
test/intersect/new_test-intersect.sh | 104 +-
test/intersect/oneRecordNoNewline.bed | 1 +
test/jaccard/a.bam | Bin 0 -> 1796 bytes
test/jaccard/aMixedStrands.bed | 12 +
test/jaccard/bMixedStrands.bed | 6 +
test/jaccard/e.bed | 1 +
test/jaccard/test-jaccard.sh | 82 +-
test/jaccard/three_blocks_match.bam | Bin 0 -> 1804 bytes
test/jaccard/three_blocks_match.bed | 1 +
test/map/d.bed | 2 +
test/map/fullFields.bam | Bin 0 -> 25813 bytes
test/map/test-map.sh | 44 +-
test/merge/a.full.bam | Bin 0 -> 1836 bytes
test/merge/a.gff | 6 +
test/merge/b.bed | 7 +
test/merge/bamCol10Collapse.txt | 112 +++
test/merge/bamCol11Collapse.txt | 112 +++
test/merge/bamCol1Collapse.txt | 112 +++
test/merge/bamCol3Collapse.txt | 112 +++
test/merge/bamCol4Mean.txt | 112 +++
test/merge/bamCol5Mean.txt | 112 +++
test/merge/bamCol6Collapse.txt | 112 +++
test/merge/bamCol7Collapse.txt | 112 +++
test/merge/bamCol8Mean.txt | 112 +++
test/merge/bamCol9Mean.txt | 112 +++
test/merge/fullFields.bam | Bin 0 -> 25813 bytes
test/merge/mergeBugTest.bed | 12 +
test/merge/mixedStrands.bed | 12 +
test/merge/precisionTest.bed | 10 +
test/merge/test-merge.sh | 391 ++++++--
test/merge/testA.vcf | 129 +++
test/merge/unsorted.bed | 7 +
test/sample/test-sample.sh | 11 +-
test/shuffle/excl.bed | 9 +
test/shuffle/incl.bed | 9 +
test/shuffle/simrep.bed | 1000 ++++++++++++++++++++
test/shuffle/test-shuffle.sh | 127 +++
test/slop/test-slop.sh | 21 +
test/test.sh | 3 +
137 files changed, 5966 insertions(+), 2116 deletions(-)
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