[med-svn] [bedtools] 06/07: 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 5d6f024fed9fc286bf58f7f769ff96c7a59c3031
Merge: 9b536ae d188b65
Author: Charles Plessy <plessy at debian.org>
Date:   Tue Jan 5 18:02:08 2016 +0900

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

 .../images/tool-glyphs/barski_binding_site.png     | Bin 0 -> 346688 bytes
 docs/content/installation.rst                      |  22 ++++---
 docs/content/tools/genomecov.rst                   |  25 ++++++++
 genomes/human.hg18.genome                          |   1 +
 genomes/human.hg19.genome                          |   1 +
 genomes/human.hg38.genome                          |   1 +
 genomes/mouse.mm10.genome                          |  67 +++++++++++++++++++++
 genomes/mouse.mm10.genome.txt                      |  66 --------------------
 genomes/mouse.mm8.genome                           |   1 +
 genomes/mouse.mm9.genome                           |   2 +-
 src/genomeCoverageBed/genomeCoverageBed.cpp        |  57 +++++++++++++++++-
 src/genomeCoverageBed/genomeCoverageBed.h          |   5 ++
 src/genomeCoverageBed/genomeCoverageMain.cpp       |  27 +++++++++
 src/intersectFile/intersectFile.cpp                |   8 ++-
 src/utils/FileRecordTools/Records/Bed4Interval.cpp |   2 +-
 src/utils/KeyListOps/KeyListOps.cpp                |   4 +-
 src/utils/KeyListOps/KeyListOpsMethods.cpp         |   8 +--
 src/utils/NewChromsweep/NewChromsweep.cpp          |  22 ++++---
 src/utils/fileType/FileRecordTypeChecker.cpp       |  10 ++-
 test/genomecov/chip.sam                            |   4 ++
 test/genomecov/pair-chip.sam                       |   4 ++
 test/genomecov/test-genomecov.sh                   |  23 +++++++
 test/groupBy/test-groupby.sh                       |   9 +++
 23 files changed, 272 insertions(+), 97 deletions(-)

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