[med-svn] [bedtools] 01/07: 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 b36ce1a99666a7e2163c306315aa8d18b98d44b6
Merge: 69e2731 91928cf
Author: Charles Plessy <plessy at debian.org>
Date:   Wed Nov 12 13:53:51 2014 +0900

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

 .gitignore                                         |   4 +
 Makefile                                           |   2 +-
 README.md                                          |   2 +-
 docs/conf.py                                       |   4 +-
 docs/content/tools/closest.rst                     |   9 +
 docs/content/tools/fisher.rst                      |   6 +-
 src/bamToFastq/bamToFastq.cpp                      |  14 +-
 src/bedtools.cpp                                   |  12 +-
 src/closestBed/Makefile                            |  32 -
 src/closestBed/closestBed.cpp                      | 289 ------
 src/closestBed/closestBed.h                        |  66 --
 src/closestBed/closestMain.cpp                     | 245 ------
 src/closestFile/Makefile                           |  44 +
 src/closestFile/closestFile.cpp                    |  41 +
 src/closestFile/closestFile.h                      |  31 +
 src/closestFile/closestMain.cpp                    | 107 +++
 src/fisher/Fisher.cpp                              | 116 ++-
 src/groupBy/groupBy.cpp                            |  55 +-
 src/utils/Contexts/ContextBase.cpp                 |   2 +-
 src/utils/Contexts/ContextClosest.cpp              | 222 +++++
 src/utils/Contexts/ContextClosest.h                |  65 ++
 src/utils/Contexts/Makefile                        |  10 +-
 .../FileReaders/SingleLineDelimTextFileReader.cpp  |  17 +
 .../FileReaders/SingleLineDelimTextFileReader.h    |  12 +
 src/utils/FileRecordTools/Records/Record.cpp       |  14 +-
 src/utils/FileRecordTools/Records/VcfRecord.cpp    |  24 +-
 src/utils/FileRecordTools/Records/VcfRecord.h      |   2 +-
 src/utils/NewChromsweep/CloseSweep.cpp             | 426 +++++++++
 src/utils/NewChromsweep/CloseSweep.h               |  53 ++
 src/utils/NewChromsweep/Makefile                   |  80 +-
 src/utils/NewChromsweep/NewChromsweep.cpp          | 506 ++++++-----
 src/utils/NewChromsweep/NewChromsweep.h            |  24 +-
 src/utils/RecordOutputMgr/Makefile                 |  78 +-
 src/utils/RecordOutputMgr/RecordOutputMgr.cpp      | 972 +++++++++++----------
 src/utils/RecordOutputMgr/RecordOutputMgr.h        | 148 ++--
 src/utils/general/ParseTools.cpp                   |  29 +-
 src/utils/version/version_release.txt              |   6 +-
 src/windowMaker/windowMakerMain.cpp                |   4 +
 test/bamtofastq/golden.fq                          |   8 +
 test/bamtofastq/golden.fq2                         |   8 +
 test/bamtofastq/test-bamtofastq.sh                 |  20 +
 test/bamtofastq/test.sam                           |   7 +
 test/closest/d_d1F.bed                             |   1 +
 test/closest/d_d1R.bed                             |   1 +
 test/closest/d_d2F.bed                             |   1 +
 test/closest/d_d2R.bed                             |   1 +
 test/closest/d_q1.bed                              |   1 +
 test/closest/d_q2.bed                              |   1 +
 test/closest/mdb1.bed                              |   4 +
 test/closest/mdb2.bed                              |   3 +
 test/closest/mdb3.bed                              |   2 +
 test/closest/mq1.bed                               |   1 +
 test/closest/test-closest.sh                       | 400 ++++++++-
 test/intersect/a_testZeroLen.bed                   |   3 +
 test/intersect/a_vcfSVtest.vcf                     |   5 +
 test/intersect/b_testZeroLen.bed                   |   3 +
 test/intersect/b_vcfSVtest.vcf                     |   5 +
 test/intersect/new_test-intersect.sh               |  50 ++
 test/merge/expFormat.bed                           |   1 +
 test/merge/test-merge.sh                           |  24 +
 test/merge/vcfSVtest.vcf                           |   5 +
 61 files changed, 2690 insertions(+), 1638 deletions(-)

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