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Cleaning popins4snake code, in particular the argument parser. Introducing a...
Cleaning popins4snake code, in particular the argument parser. Introducing a merge-locations command by splitting this task from place-refalign.
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- .gitmodules 3 additions, 0 deletions.gitmodules
- external/bifrost 1 addition, 0 deletionsexternal/bifrost
- src/argument_parsing.h 266 additions, 169 deletionssrc/argument_parsing.h
- src/crop_unmapped.h 1 addition, 1 deletionsrc/crop_unmapped.h
- src/location.h 0 additions, 2 deletionssrc/location.h
- src/popins2_crop_unmapped.h 6 additions, 12 deletionssrc/popins2_crop_unmapped.h
- src/popins2_find_locations.h 80 additions, 0 deletionssrc/popins2_find_locations.h
- src/popins2_genotype.h 4 additions, 4 deletionssrc/popins2_genotype.h
- src/popins2_merge.h 0 additions, 2 deletionssrc/popins2_merge.h
- src/popins2_merge_and_set_mate.h 6 additions, 6 deletionssrc/popins2_merge_and_set_mate.h
- src/popins2_merge_locations.h 70 additions, 0 deletionssrc/popins2_merge_locations.h
- src/popins2_place.h 2 additions, 47 deletionssrc/popins2_place.h
- src/popins4snake.cpp 7 additions, 5 deletionssrc/popins4snake.cpp
- src/popins_find_locations.h 0 additions, 312 deletionssrc/popins_find_locations.h
- src/variant_caller.h 1 addition, 1 deletionsrc/variant_caller.h
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