First pass at new, consolidated CLI.
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- Makefile 14 additions, 0 deletionsMakefile
- src/annotateBed/Makefile 1 addition, 5 deletionssrc/annotateBed/Makefile
- src/annotateBed/annotateMain.cpp 10 additions, 12 deletionssrc/annotateBed/annotateMain.cpp
- src/bamToBed/Makefile 1 addition, 5 deletionssrc/bamToBed/Makefile
- src/bamToBed/bamToBed.cpp 11 additions, 12 deletionssrc/bamToBed/bamToBed.cpp
- src/bed12ToBed6/Makefile 1 addition, 6 deletionssrc/bed12ToBed6/Makefile
- src/bed12ToBed6/bed12ToBed6.cpp 9 additions, 10 deletionssrc/bed12ToBed6/bed12ToBed6.cpp
- src/bedToBam/Makefile 1 addition, 6 deletionssrc/bedToBam/Makefile
- src/bedToBam/bedToBam.cpp 14 additions, 15 deletionssrc/bedToBam/bedToBam.cpp
- src/bedToIgv/Makefile 1 addition, 6 deletionssrc/bedToIgv/Makefile
- src/bedToIgv/bedToIgv.cpp 11 additions, 12 deletionssrc/bedToIgv/bedToIgv.cpp
- src/bedpeToBam/Makefile 1 addition, 6 deletionssrc/bedpeToBam/Makefile
- src/bedpeToBam/bedpeToBam.cpp 18 additions, 23 deletionssrc/bedpeToBam/bedpeToBam.cpp
- src/bedpeToBam/notes.txt 44 additions, 0 deletionssrc/bedpeToBam/notes.txt
- src/bedtools.cpp 138 additions, 31 deletionssrc/bedtools.cpp
- src/closestBed/Makefile 1 addition, 5 deletionssrc/closestBed/Makefile
- src/closestBed/closestMain.cpp 21 additions, 22 deletionssrc/closestBed/closestMain.cpp
- src/complementBed/Makefile 1 addition, 5 deletionssrc/complementBed/Makefile
- src/complementBed/complementMain.cpp 10 additions, 12 deletionssrc/complementBed/complementMain.cpp
- src/coverageBed/Makefile 1 addition, 5 deletionssrc/coverageBed/Makefile
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