[med-svn] [bedtools] branch master updated (030bbed -> 9b536ae)

[Charles Plessy]

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plessy pushed a change to branch master
in repository bedtools.

      from  030bbed   Merge branch 'master' of https://github.com/arq5x/bedtools2
       new  554c097   Fixed bug281: -S not working in closest. Added unit tests.
       new  e84011c   Addressed bug 268: slowdown with -iu
       new  b03556e   still working on bug268, progress made
       new  7ba9c36   More fixes to closest for bug268; disallowed stranded ops on unstranded files for all tools.
       new  96a2d84   update conf.py to avoid sphinx build error on RTD.
       new  788a6b6   handle null record when db is bed6+. affected -wao, -loj, closest.
       new  93cb0b1   remove memory leak in NewChromSweep::closeOut
       new  f66a564   Update README.md
       new  11640d8   Update README.md
       new  c3ba7be   Update README.md
       new  285c3ac   Update README.md
       new  0686eea   Merge branch 'master' of https://github.com/arq5x/bedtools2
       new  d22594e   Check for non-empty vector
       new  7f765bc   Merge pull request #306 from gatoravi/master
       new  6de430d   issue #303. fix memory leak in groupby.
       new  61b9c41   Merge remote-tracking branch 'upstream/master'
       new  ef9f42a   Fixed bug #317, groupBy failed to recognize integers with decimals
       new  f9ef58f   General fix for #317 - for groupBy, override non-bam files' type
       new  e392a61   Merge pull request #294 from nkindlon/master
       new  b35341c   Move "using namespace std" after #includes
       new  67aca77   Use ostringstream to format filename
       new  3d31735   Merge pull request #320 from jmarshall/warnings4
       new  9b536ae   Merge branch 'master' of https://github.com/arq5x/bedtools2

The 23 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 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(-)
 create mode 100644 test/closest/bug281_a.flip.medium.bed
 create mode 100644 test/closest/bug281_a.medium.bed
 create mode 100644 test/closest/bug281_b.bed
 create mode 100644 test/closest/bug281_b.flip.bed

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