[med-svn] [bedtools] 01/13: Merge tag 'v2.19.1' into debian/unstable

[Charles Plessy]

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

commit 479e63b57fd8660c4ad174ade3d17bfe58b55ee3
Merge: f93eb83 a3fefa2
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Mar 7 07:57:28 2014 +0900

    Merge tag 'v2.19.1' into debian/unstable

 Makefile                                           |   1 +
 .../images/tool-glyphs/map-speed-comparo.png       | Bin 0 -> 41233 bytes
 docs/content/tools/map.rst                         |  35 +-
 genomes/mouse.mm10.genome.txt                      |  66 ++++
 src/intersectFile/Makefile                         |   1 +
 src/mapFile/Makefile                               |   1 +
 src/mapFile/mapFile.cpp                            |  67 +---
 src/mapFile/mapFile.h                              |  85 +----
 src/mapFile/mapMain.cpp                            | 138 --------
 src/nekSandbox1/Makefile                           |   1 +
 src/regressTest/Makefile                           |   1 +
 src/sampleFile/Makefile                            |   1 +
 src/utils/BinTree/Makefile                         |   1 +
 src/utils/Contexts/ContextBase.cpp                 | 132 +++++++-
 src/utils/Contexts/ContextBase.h                   |  21 +-
 src/utils/Contexts/ContextIntersect.h              |   2 +
 src/utils/Contexts/ContextMap.cpp                  |  93 +-----
 src/utils/Contexts/ContextMap.h                    |  20 +-
 src/utils/Contexts/Makefile                        |   1 +
 src/utils/FileRecordTools/Records/BamRecord.cpp    |   5 +
 src/utils/FileRecordTools/Records/BamRecord.h      |   1 +
 .../FileRecordTools/Records/Bed12Interval.cpp      |  26 ++
 src/utils/FileRecordTools/Records/Bed12Interval.h  |   1 +
 src/utils/FileRecordTools/Records/Bed3Interval.cpp |  20 ++
 src/utils/FileRecordTools/Records/Bed3Interval.h   |   2 +
 src/utils/FileRecordTools/Records/Bed4Interval.cpp |   5 +
 src/utils/FileRecordTools/Records/Bed4Interval.h   |   1 +
 src/utils/FileRecordTools/Records/Bed5Interval.cpp |  13 +
 src/utils/FileRecordTools/Records/Bed5Interval.h   |   1 +
 src/utils/FileRecordTools/Records/Bed6Interval.cpp |  17 +
 src/utils/FileRecordTools/Records/Bed6Interval.h   |   1 +
 .../FileRecordTools/Records/BedGraphInterval.cpp   |  11 +
 .../FileRecordTools/Records/BedGraphInterval.h     |   1 +
 .../FileRecordTools/Records/BedPlusInterval.cpp    |  15 +
 .../FileRecordTools/Records/BedPlusInterval.h      |   2 +
 src/utils/FileRecordTools/Records/GffRecord.cpp    |  36 ++
 src/utils/FileRecordTools/Records/GffRecord.h      |   1 +
 src/utils/FileRecordTools/Records/Record.cpp       |   6 +-
 src/utils/FileRecordTools/Records/Record.h         |   2 +
 src/utils/GenomeFile/Makefile                      |   1 +
 src/utils/KeyListOps/KeyListOps.cpp                | 364 ++++++++++++++++++++
 src/utils/KeyListOps/KeyListOps.h                  |  54 +++
 src/utils/KeyListOps/KeyListOpsMethods.cpp         | 368 +++++++++++++++++++++
 src/utils/KeyListOps/KeyListOpsMethods.h           | 113 +++++++
 src/utils/{RecordOutputMgr => KeyListOps}/Makefile |  12 +-
 src/utils/NewChromsweep/Makefile                   |   1 +
 src/utils/RecordOutputMgr/Makefile                 |   1 +
 src/utils/general/Makefile                         |   2 +-
 src/utils/general/QuickString.cpp                  |  65 ++++
 src/utils/general/QuickString.h                    |  19 ++
 src/utils/version/version_release.txt              |   6 +-
 test/intersect/test-intersect.sh                   |  11 +-
 test/map/test-map.sh                               | 148 +++++++--
 53 files changed, 1567 insertions(+), 432 deletions(-)

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