[med-svn] [bedtools] 05/07: Merge branch 'master' of https://github.com/arq5x/bedtools2

[Andreas Tille]

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tille pushed a commit to branch upstream
in repository bedtools.

commit 9b536aea2258b2181f3d10eb0f540aa636076108
Merge: 030bbed 3d31735
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Dec 28 13:47:11 2015 +0900

    Merge branch 'master' of https://github.com/arq5x/bedtools2

 README.md                                      |  15 +-
 docs/conf.py                                   |   2 +-
 src/groupBy/groupBy.cpp                        |   8 +-
 src/split/splitBed.cpp                         |  11 +-
 src/utils/Contexts/ContextBase.cpp             |  32 ++-
 src/utils/Contexts/ContextBase.h               |   2 +
 src/utils/Contexts/ContextIntersect.cpp        |   4 +
 src/utils/Contexts/ContextJaccard.cpp          |  20 --
 src/utils/Contexts/ContextMerge.cpp            |  11 +-
 src/utils/FileRecordTools/FileRecordMgr.cpp    |  11 +-
 src/utils/FileRecordTools/FileRecordMgr.h      |   2 +
 src/utils/FileRecordTools/Records/PlusFields.h |   4 +-
 src/utils/NewChromsweep/CloseSweep.cpp         | 313 +++++++++++++++----------
 src/utils/NewChromsweep/CloseSweep.h           |  39 ++-
 src/utils/NewChromsweep/NewChromsweep.cpp      |   5 +-
 src/utils/RecordOutputMgr/RecordOutputMgr.cpp  |   7 +-
 src/utils/bedFile/bedFile.cpp                  |   2 +-
 src/utils/fileType/FileRecordTypeChecker.cpp   |   7 +-
 src/utils/general/ParseTools.cpp               |  15 +-
 src/utils/general/ParseTools.h                 |   1 +
 test/closest/bug281_a.flip.medium.bed          |   2 +
 test/closest/bug281_a.medium.bed               |   2 +
 test/closest/bug281_b.bed                      |   4 +
 test/closest/bug281_b.flip.bed                 |   4 +
 test/closest/test-closest.sh                   |  98 ++++++++
 25 files changed, 435 insertions(+), 186 deletions(-)

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