Corrected commnad line parsing for all tools.
There was a problem with the way args with a value were being parsed.
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- src/closestBed/closestMain.cpp 15 additions, 9 deletionssrc/closestBed/closestMain.cpp
- src/complementBed/complementMain.cpp 10 additions, 6 deletionssrc/complementBed/complementMain.cpp
- src/coverageBed/coverageMain.cpp 10 additions, 6 deletionssrc/coverageBed/coverageMain.cpp
- src/fastaFromBed/fastaFromBedMain.cpp 15 additions, 9 deletionssrc/fastaFromBed/fastaFromBedMain.cpp
- src/genomeCoverageBed/genomeCoverageMain.cpp 14 additions, 12 deletionssrc/genomeCoverageBed/genomeCoverageMain.cpp
- src/intersectBed/intersectMain.cpp 10 additions, 8 deletionssrc/intersectBed/intersectMain.cpp
- src/linksBed/linksMain.cpp 17 additions, 9 deletionssrc/linksBed/linksMain.cpp
- src/maskFastaFromBed/maskFastaFromBedMain.cpp 15 additions, 9 deletionssrc/maskFastaFromBed/maskFastaFromBedMain.cpp
- src/mergeBed/mergeMain.cpp 10 additions, 6 deletionssrc/mergeBed/mergeMain.cpp
- src/pairToBed/pairToBedMain.cpp 10 additions, 6 deletionssrc/pairToBed/pairToBedMain.cpp
- src/pairToPair/pairToPairMain.cpp 8 additions, 7 deletionssrc/pairToPair/pairToPairMain.cpp
- src/shuffleBed/shuffleBedMain.cpp 20 additions, 12 deletionssrc/shuffleBed/shuffleBedMain.cpp
- src/slopBed/slopBedMain.cpp 26 additions, 17 deletionssrc/slopBed/slopBedMain.cpp
- src/sortBed/sortMain.cpp 5 additions, 9 deletionssrc/sortBed/sortMain.cpp
- src/subtractBed/subtractMain.cpp 7 additions, 5 deletionssrc/subtractBed/subtractMain.cpp
- src/windowBed/windowMain.cpp 26 additions, 16 deletionssrc/windowBed/windowMain.cpp
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