Big commit.
1. Added new version of BamTools supporting uncompressed BAM. 2. Added -ubam option to intersectBed. 3. First functional release of annotateBed. 4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.
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- Makefile 2 additions, 1 deletionMakefile
- src/annotateBed/Makefile 8 additions, 5 deletionssrc/annotateBed/Makefile
- src/annotateBed/annotateBed.cpp 164 additions, 99 deletionssrc/annotateBed/annotateBed.cpp
- src/annotateBed/annotateBed.h 38 additions, 16 deletionssrc/annotateBed/annotateBed.h
- src/annotateBed/annotateMain.cpp 71 additions, 36 deletionssrc/annotateBed/annotateMain.cpp
- src/bamToBed/bamToBed.cpp 8 additions, 8 deletionssrc/bamToBed/bamToBed.cpp
- src/intersectBed/intersectBed.cpp 4 additions, 3 deletionssrc/intersectBed/intersectBed.cpp
- src/intersectBed/intersectBed.h 2 additions, 1 deletionsrc/intersectBed/intersectBed.h
- src/intersectBed/intersectMain.cpp 5 additions, 2 deletionssrc/intersectBed/intersectMain.cpp
- src/pairToBed/pairToBed.h 3 additions, 3 deletionssrc/pairToBed/pairToBed.h
- src/utils/BamTools/BGZF.cpp 60 additions, 49 deletionssrc/utils/BamTools/BGZF.cpp
- src/utils/BamTools/BGZF.h 65 additions, 69 deletionssrc/utils/BamTools/BGZF.h
- src/utils/BamTools/BamAux.h 591 additions, 339 deletionssrc/utils/BamTools/BamAux.h
- src/utils/BamTools/BamIndex.cpp 5 additions, 3 deletionssrc/utils/BamTools/BamIndex.cpp
- src/utils/BamTools/BamIndex.h 4 additions, 1 deletionsrc/utils/BamTools/BamIndex.h
- src/utils/BamTools/BamMultiReader.cpp 1 addition, 1 deletionsrc/utils/BamTools/BamMultiReader.cpp
- src/utils/BamTools/BamReader.cpp 3 additions, 1 deletionsrc/utils/BamTools/BamReader.cpp
- src/utils/BamTools/BamWriter.cpp 11 additions, 7 deletionssrc/utils/BamTools/BamWriter.cpp
- src/utils/BamTools/BamWriter.h 5 additions, 2 deletionssrc/utils/BamTools/BamWriter.h
- src/utils/bedFile/bedFile.cpp 68 additions, 0 deletionssrc/utils/bedFile/bedFile.cpp
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