[med-svn] [bedtools] 07/14: Merge pull request #41 from nkindlon/master

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a commit to branch master
in repository bedtools.

commit 1a0737dfa2e55f5a8c507705211f2edf3e8c0a07
Merge: 4793c98 af1113e
Author: Aaron Quinlan <aaronquinlan at gmail.com>
Date:   Sat Mar 1 09:37:09 2014 -0500

    Merge pull request #41 from nkindlon/master
    
    Refactored KeyListOps, Context, mapFile to make KeyListOps reusable by other tools

 src/intersectFile/Makefile                         |   1 +
 src/mapFile/mapFile.cpp                            | 168 +-----
 src/mapFile/mapFile.h                              |   5 -
 src/nekSandbox1/Makefile                           |   1 +
 src/regressTest/Makefile                           |   1 +
 src/sampleFile/Makefile                            |   1 +
 src/utils/BinTree/Makefile                         |   1 +
 src/utils/Contexts/ContextBase.cpp                 | 113 +++-
 src/utils/Contexts/ContextBase.h                   |  17 +
 src/utils/Contexts/ContextMap.cpp                  | 148 +----
 src/utils/Contexts/ContextMap.h                    |  31 +-
 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                | 635 ++++++++++-----------
 src/utils/KeyListOps/KeyListOps.h                  | 113 +---
 .../{KeyListOps.cpp => KeyListOpsMethods.cpp}      |  99 +---
 .../{KeyListOps.h => KeyListOpsMethods.h}          |  24 +-
 src/utils/KeyListOps/Makefile                      |  12 +-
 src/utils/NewChromsweep/Makefile                   |   1 +
 src/utils/RecordOutputMgr/Makefile                 |   1 +
 test/map/test-map.sh                               | 121 +++-
 40 files changed, 815 insertions(+), 846 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git