├── Makefile ├── README.md ├── examples └── hg19.HindIII_fragments.bed └── src ├── BAMtoSparseMatrix.py ├── HIFI ├── HIFI.cpp ├── HIFI_MyMatrix.h ├── HIFI_misc.h ├── HIFI_options.cpp ├── HIFI_options.h ├── SparseToFixed.py ├── callPeaks.cpp ├── parseHIFIoutput.py └── plotHIFIoutput.py /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/README.md -------------------------------------------------------------------------------- /examples/hg19.HindIII_fragments.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/examples/hg19.HindIII_fragments.bed -------------------------------------------------------------------------------- /src/BAMtoSparseMatrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/BAMtoSparseMatrix.py -------------------------------------------------------------------------------- /src/HIFI: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI -------------------------------------------------------------------------------- /src/HIFI.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI.cpp -------------------------------------------------------------------------------- /src/HIFI_MyMatrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI_MyMatrix.h -------------------------------------------------------------------------------- /src/HIFI_misc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI_misc.h -------------------------------------------------------------------------------- /src/HIFI_options.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI_options.cpp -------------------------------------------------------------------------------- /src/HIFI_options.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/HIFI_options.h -------------------------------------------------------------------------------- /src/SparseToFixed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/SparseToFixed.py -------------------------------------------------------------------------------- /src/callPeaks.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/callPeaks.cpp -------------------------------------------------------------------------------- /src/parseHIFIoutput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/parseHIFIoutput.py -------------------------------------------------------------------------------- /src/plotHIFIoutput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlanchetteLab/HIFI/HEAD/src/plotHIFIoutput.py --------------------------------------------------------------------------------