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commit 1a0737dfa2e55f5a8c507705211f2edf3e8c0a07 Merge: 4793c98 af1113e Author: Aaron Quinlan <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
