Large, performance-related commit.
1. Created separate structs for BED and BEDCOV in order to reduce memory consumption. Savings of ~30%. 2. Changed the binning approach to make 16kb bins the most granular. IntersectBed is now 1/3 faster as a result. 3. Templated the parsing and reporting functions in bedFile. Had to move them to the header file to avoid linker complications. 4. Added CHRPOS as a common type.
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- ._Makefile.uZs1Vt 0 additions, 0 deletions._Makefile.uZs1Vt
- ._README.89gPvU 0 additions, 0 deletions._README.89gPvU
- src/coverageBed/coverageBed.cpp 12 additions, 14 deletionssrc/coverageBed/coverageBed.cpp
- src/intersectBed/intersectBed.cpp 5 additions, 8 deletionssrc/intersectBed/intersectBed.cpp
- src/intersectBed/intersectBed.h 1 addition, 1 deletionsrc/intersectBed/intersectBed.h
- src/utils/bedFile/Makefile 1 addition, 1 deletionsrc/utils/bedFile/Makefile
- src/utils/bedFile/bedFile.cpp 109 additions, 647 deletionssrc/utils/bedFile/bedFile.cpp
- src/utils/bedFile/bedFile.h 621 additions, 66 deletionssrc/utils/bedFile/bedFile.h
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