[med-svn] [bedtools] 02/05: Merge tag '2.20.1' into debian/unstable

Andreas Tille tille at debian.org
Fri Jun 6 20:21:03 UTC 2014


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tille pushed a commit to branch debian/unstable
in repository bedtools.

commit e1da9e151cc5b7302c19dd01df185a221481133d
Merge: 68dfd72 a0d28a5
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 6 21:50:13 2014 +0200

    Merge tag '2.20.1' into debian/unstable
    
    Upstream version 2.20.1

 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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