Large commit
1. Reset BED.strand to be string instead of char in the interest of generality. 2. Fixed bug in genomeCoverageBed where NULL entries where genome summaries were err. reported with -bga. 3. Fixed bug in closestBed where NULL entries were err. reported when BED > 6. 4. Standardized the Open, Get, Close idiom per improvements from Gordon Assaf. 5. Add "split" logic to bamToBed.
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- .cproject 0 additions, 0 deletions.cproject
- .project 0 additions, 0 deletions.project
- LICENSE 0 additions, 0 deletionsLICENSE
- RELEASE_HISTORY 0 additions, 0 deletionsRELEASE_HISTORY
- data/knownGene.hg18.chr21.bed 0 additions, 0 deletionsdata/knownGene.hg18.chr21.bed
- genomes/human.hg18.genome 0 additions, 0 deletionsgenomes/human.hg18.genome
- genomes/human.hg19.genome 0 additions, 0 deletionsgenomes/human.hg19.genome
- genomes/mouse.mm8.genome 0 additions, 0 deletionsgenomes/mouse.mm8.genome
- genomes/mouse.mm9.genome 0 additions, 0 deletionsgenomes/mouse.mm9.genome
- src/bamFillMateSeq/Makefile 0 additions, 45 deletionssrc/bamFillMateSeq/Makefile
- src/bamFillMateSeq/bamFillMateSeq.cpp 0 additions, 294 deletionssrc/bamFillMateSeq/bamFillMateSeq.cpp
- src/bamToBed/Makefile 2 additions, 2 deletionssrc/bamToBed/Makefile
- src/bamToBed/bamToBed.cpp 53 additions, 23 deletionssrc/bamToBed/bamToBed.cpp
- src/bedToBam/Makefile 2 additions, 2 deletionssrc/bedToBam/Makefile
- src/bedToBam/bedToBam.cpp 7 additions, 4 deletionssrc/bedToBam/bedToBam.cpp
- src/closestBed/closestBed.cpp 5 additions, 31 deletionssrc/closestBed/closestBed.cpp
- src/complementBed/complementBed.cpp 12 additions, 15 deletionssrc/complementBed/complementBed.cpp
- src/fastaFromBed/fastaFromBed.cpp 1 addition, 1 deletionsrc/fastaFromBed/fastaFromBed.cpp
- src/genomeCoverageBed/genomeCoverageBed.cpp 1 addition, 1 deletionsrc/genomeCoverageBed/genomeCoverageBed.cpp
- src/linksBed/linksBed.cpp 1 addition, 4 deletionssrc/linksBed/linksBed.cpp
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