├── .gitignore ├── LICENSE ├── README.md ├── bin ├── ALLHiC_linkage_distribution.py ├── ALLHiC_mono_allele_minimap.py ├── ALLHiC_partition.py ├── ALLHiC_pip.sh ├── ALLHiC_plot.py ├── ALLHiC_prune ├── ALLHiC_rescue.py └── partition_gmap.py └── src ├── ALLHiC_prune.cpp ├── Makefile ├── Prune.cpp ├── Prune.h └── htslib-1.17.tar.bz2 /.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore Mac system file 2 | .DS_Store 3 | .vscode 4 | htslib-1.17 5 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/README.md -------------------------------------------------------------------------------- /bin/ALLHiC_linkage_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_linkage_distribution.py -------------------------------------------------------------------------------- /bin/ALLHiC_mono_allele_minimap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_mono_allele_minimap.py -------------------------------------------------------------------------------- /bin/ALLHiC_partition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_partition.py -------------------------------------------------------------------------------- /bin/ALLHiC_pip.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_pip.sh -------------------------------------------------------------------------------- /bin/ALLHiC_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_plot.py -------------------------------------------------------------------------------- /bin/ALLHiC_prune: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_prune -------------------------------------------------------------------------------- /bin/ALLHiC_rescue.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/ALLHiC_rescue.py -------------------------------------------------------------------------------- /bin/partition_gmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/bin/partition_gmap.py -------------------------------------------------------------------------------- /src/ALLHiC_prune.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/src/ALLHiC_prune.cpp -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/src/Makefile -------------------------------------------------------------------------------- /src/Prune.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/src/Prune.cpp -------------------------------------------------------------------------------- /src/Prune.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/src/Prune.h -------------------------------------------------------------------------------- /src/htslib-1.17.tar.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sc-zhang/ALLHiC_extensions/HEAD/src/htslib-1.17.tar.bz2 --------------------------------------------------------------------------------