├── .gitignore ├── CHANGELOG.txt ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin ├── epic2 ├── epic2-bw └── epic2-df ├── epic2 ├── __init__.py ├── bigwig.py ├── chromsizes │ ├── ailMel1.chromsizes │ ├── anoCar2.chromsizes │ ├── apiMel1.chromsizes │ ├── aplCal1.chromsizes │ ├── aquChr2.chromsizes │ ├── balAcu1.chromsizes │ ├── braFlo1.chromsizes │ ├── calJac1.chromsizes │ ├── calJac3.chromsizes │ ├── cavPor3.chromsizes │ ├── ce10.chromsizes │ ├── ce11.chromsizes │ ├── cerSim1.chromsizes │ ├── chlSab2.chromsizes │ ├── chrPic1.chromsizes │ ├── danRer10.chromsizes │ ├── danRer3.chromsizes │ ├── danRer4.chromsizes │ ├── danRer5.chromsizes │ ├── danRer6.chromsizes │ ├── danRer7.chromsizes │ ├── dm3.chromsizes │ ├── dm6.chromsizes │ ├── echTel2.chromsizes │ ├── equCab1.chromsizes │ ├── equCab2.chromsizes │ ├── eriEur1.chromsizes │ ├── eriEur2.chromsizes │ ├── fr1.chromsizes │ ├── fr2.chromsizes │ ├── galVar1.chromsizes │ ├── gasAcu1.chromsizes │ ├── geoFor1.chromsizes │ ├── gorGor3.chromsizes │ ├── gorGor4.chromsizes │ ├── gorGor5.chromsizes │ ├── hetGla1.chromsizes │ ├── hetGla2.chromsizes │ ├── hg18.chromsizes │ ├── hg19.chromsizes │ ├── hg38.chromsizes │ ├── loxAfr3.chromsizes │ ├── macEug2.chromsizes │ ├── melGal1.chromsizes │ ├── melGal5.chromsizes │ ├── micMur2.chromsizes │ ├── mm10.chromsizes │ ├── mm9.chromsizes │ ├── monDom4.chromsizes │ ├── monDom5.chromsizes │ ├── myoLuc2.chromsizes │ ├── nanPar1.chromsizes │ ├── nasLar1.chromsizes │ ├── nomLeu1.chromsizes │ ├── nomLeu2.chromsizes │ ├── nomLeu3.chromsizes │ ├── ochPri3.chromsizes │ ├── oreNil2.chromsizes │ ├── ornAna1.chromsizes │ ├── ornAna2.chromsizes │ ├── oryCun2.chromsizes │ ├── oryLat2.chromsizes │ ├── oviAri1.chromsizes │ ├── oviAri3.chromsizes │ ├── papAnu2.chromsizes │ ├── petMar1.chromsizes │ ├── petMar2.chromsizes │ ├── ponAbe2.chromsizes │ ├── priPac1.chromsizes │ ├── rheMac2.chromsizes │ ├── rheMac3.chromsizes │ ├── rheMac8.chromsizes │ ├── rhiRox1.chromsizes │ ├── rn4.chromsizes │ ├── rn5.chromsizes │ ├── rn6.chromsizes │ ├── sacCer1.chromsizes │ ├── sacCer2.chromsizes │ ├── sacCer3.chromsizes │ ├── saiBol1.chromsizes │ ├── sorAra2.chromsizes │ ├── speTri2.chromsizes │ ├── strPur1.chromsizes │ ├── strPur2.chromsizes │ ├── susScr2.chromsizes │ ├── susScr3.chromsizes │ ├── taeGut1.chromsizes │ ├── taeGut2.chromsizes │ ├── tarSyr2.chromsizes │ ├── tetNig1.chromsizes │ ├── tetNig2.chromsizes │ ├── triMan1.chromsizes │ ├── xenTro3.chromsizes │ └── xenTro7.chromsizes ├── effective_sizes │ ├── ailMel1_100.txt │ ├── ailMel1_36.txt │ ├── ailMel1_50.txt │ ├── ailMel1_75.txt │ ├── anoCar2_100.txt │ ├── anoCar2_36.txt │ ├── anoCar2_50.txt │ ├── anoCar2_75.txt │ ├── aplCal1_100.txt │ ├── aplCal1_36.txt │ ├── aplCal1_50.txt │ ├── aplCal1_75.txt │ ├── aquChr2_100.txt │ ├── aquChr2_36.txt │ ├── aquChr2_50.txt │ ├── aquChr2_75.txt │ ├── balAcu1_100.txt │ ├── balAcu1_36.txt │ ├── balAcu1_50.txt │ ├── balAcu1_75.txt │ ├── braFlo1_100.txt │ ├── braFlo1_36.txt │ ├── braFlo1_50.txt │ ├── braFlo1_75.txt │ ├── calJac1_100.txt │ ├── calJac1_36.txt │ ├── calJac1_50.txt │ ├── calJac1_75.txt │ ├── calJac3_100.txt │ ├── calJac3_36.txt │ ├── calJac3_50.txt │ ├── calJac3_75.txt │ ├── cavPor3_100.txt │ ├── cavPor3_36.txt │ ├── cavPor3_50.txt │ ├── cavPor3_75.txt │ ├── ce10_100.txt │ ├── ce10_36.txt │ ├── ce10_50.txt │ ├── ce10_75.txt │ ├── ce11_100.txt │ ├── ce11_36.txt │ ├── ce11_50.txt │ ├── ce11_75.txt │ ├── cerSim1_100.txt │ ├── cerSim1_36.txt │ ├── cerSim1_50.txt │ ├── cerSim1_75.txt │ ├── chlSab2_100.txt │ ├── chlSab2_36.txt │ ├── chlSab2_50.txt │ ├── chlSab2_75.txt │ ├── chrPic1_100.txt │ ├── chrPic1_36.txt │ ├── chrPic1_50.txt │ ├── chrPic1_75.txt │ ├── danRer10_100.txt │ ├── danRer10_36.txt │ ├── danRer10_50.txt │ ├── danRer10_75.txt │ ├── danRer3_100.txt │ ├── danRer3_36.txt │ ├── danRer3_50.txt │ ├── danRer3_75.txt │ ├── danRer4_100.txt │ ├── danRer4_36.txt │ ├── danRer4_50.txt │ ├── danRer4_75.txt │ ├── danRer5_100.txt │ ├── danRer5_36.txt │ ├── danRer5_50.txt │ ├── danRer5_75.txt │ ├── danRer6_100.txt │ ├── danRer6_36.txt │ ├── danRer6_50.txt │ ├── danRer6_75.txt │ ├── danRer7_100.txt │ ├── danRer7_36.txt │ ├── danRer7_50.txt │ ├── danRer7_75.txt │ ├── dm3_100.txt │ ├── dm3_36.txt │ ├── dm3_50.txt │ ├── dm3_75.txt │ ├── dm6_100.txt │ ├── dm6_36.txt │ ├── dm6_50.txt │ ├── dm6_75.txt │ ├── echTel2_100.txt │ ├── echTel2_36.txt │ ├── echTel2_50.txt │ ├── echTel2_75.txt │ ├── equCab1_100.txt │ ├── equCab1_36.txt │ ├── equCab1_50.txt │ ├── equCab1_75.txt │ ├── equCab2_100.txt │ ├── equCab2_36.txt │ ├── equCab2_50.txt │ ├── equCab2_75.txt │ ├── eriEur1_100.txt │ ├── eriEur1_36.txt │ ├── eriEur1_50.txt │ ├── eriEur1_75.txt │ ├── eriEur2_100.txt │ ├── eriEur2_36.txt │ ├── eriEur2_50.txt │ ├── eriEur2_75.txt │ ├── fr1_100.txt │ ├── fr1_36.txt │ ├── fr1_50.txt │ ├── fr1_75.txt │ ├── fr2_100.txt │ ├── fr2_36.txt │ ├── fr2_50.txt │ ├── fr2_75.txt │ ├── galVar1_100.txt │ ├── galVar1_36.txt │ ├── galVar1_50.txt │ ├── galVar1_75.txt │ ├── gasAcu1_100.txt │ ├── gasAcu1_36.txt │ ├── gasAcu1_50.txt │ ├── gasAcu1_75.txt │ ├── geoFor1_100.txt │ ├── geoFor1_36.txt │ ├── geoFor1_50.txt │ ├── geoFor1_75.txt │ ├── gorGor3_100.txt │ ├── gorGor3_36.txt │ ├── gorGor3_50.txt │ ├── gorGor3_75.txt │ ├── gorGor4_100.txt │ ├── gorGor4_36.txt │ ├── gorGor4_50.txt │ ├── gorGor4_75.txt │ ├── gorGor5_100.txt │ ├── gorGor5_36.txt │ ├── gorGor5_50.txt │ ├── gorGor5_75.txt │ ├── hetGla1_100.txt │ ├── hetGla1_36.txt │ ├── hetGla1_50.txt │ ├── hetGla1_75.txt │ ├── hetGla2_100.txt │ ├── hetGla2_36.txt │ ├── hetGla2_50.txt │ ├── hetGla2_75.txt │ ├── hg18_100.txt │ ├── hg18_36.txt │ ├── hg18_50.txt │ ├── hg18_75.txt │ ├── hg19_100.txt │ ├── hg19_36.txt │ ├── hg19_50.txt │ ├── hg19_75.txt │ ├── hg38_100.txt │ ├── hg38_36.txt │ ├── hg38_50.txt │ ├── hg38_75.txt │ ├── macEug2_100.txt │ ├── macEug2_36.txt │ ├── macEug2_50.txt │ ├── macEug2_75.txt │ ├── melGal1_100.txt │ ├── melGal1_36.txt │ ├── melGal1_50.txt │ ├── melGal1_75.txt │ ├── melGal5_100.txt │ ├── melGal5_36.txt │ ├── melGal5_50.txt │ ├── melGal5_75.txt │ ├── micMur2_100.txt │ ├── micMur2_36.txt │ ├── micMur2_50.txt │ ├── micMur2_75.txt │ ├── mm10_100.txt │ ├── mm10_36.txt │ ├── mm10_50.txt │ ├── mm10_75.txt │ ├── mm9_100.txt │ ├── mm9_36.txt │ ├── mm9_50.txt │ ├── mm9_75.txt │ ├── monDom4_100.txt │ ├── monDom4_36.txt │ ├── monDom4_50.txt │ ├── monDom4_75.txt │ ├── monDom5_100.txt │ ├── monDom5_36.txt │ ├── monDom5_50.txt │ ├── monDom5_75.txt │ ├── myoLuc2_100.txt │ ├── myoLuc2_36.txt │ ├── myoLuc2_50.txt │ ├── myoLuc2_75.txt │ ├── nanPar1_100.txt │ ├── nanPar1_36.txt │ ├── nanPar1_50.txt │ ├── nanPar1_75.txt │ ├── nasLar1_100.txt │ ├── nasLar1_36.txt │ ├── nasLar1_50.txt │ ├── nasLar1_75.txt │ ├── nomLeu1_100.txt │ ├── nomLeu1_36.txt │ ├── nomLeu1_50.txt │ ├── nomLeu1_75.txt │ ├── nomLeu2_100.txt │ ├── nomLeu2_36.txt │ ├── nomLeu2_50.txt │ ├── nomLeu2_75.txt │ ├── nomLeu3_100.txt │ ├── nomLeu3_36.txt │ ├── nomLeu3_50.txt │ ├── nomLeu3_75.txt │ ├── ochPri3_100.txt │ ├── ochPri3_36.txt │ ├── ochPri3_50.txt │ ├── ochPri3_75.txt │ ├── oreNil2_100.txt │ ├── oreNil2_36.txt │ ├── oreNil2_50.txt │ ├── oreNil2_75.txt │ ├── ornAna1_100.txt │ ├── ornAna1_36.txt │ ├── ornAna1_50.txt │ ├── ornAna1_75.txt │ ├── ornAna2_100.txt │ ├── ornAna2_36.txt │ ├── ornAna2_50.txt │ ├── ornAna2_75.txt │ ├── oryCun2_100.txt │ ├── oryCun2_36.txt │ ├── oryCun2_50.txt │ ├── oryCun2_75.txt │ ├── oryLat2_100.txt │ ├── oryLat2_36.txt │ ├── oryLat2_50.txt │ ├── oryLat2_75.txt │ ├── oviAri1_100.txt │ ├── oviAri1_36.txt │ ├── oviAri1_50.txt │ ├── oviAri1_75.txt │ ├── oviAri3_100.txt │ ├── oviAri3_36.txt │ ├── oviAri3_50.txt │ ├── oviAri3_75.txt │ ├── petMar1_100.txt │ ├── petMar1_36.txt │ ├── petMar1_50.txt │ ├── petMar1_75.txt │ ├── petMar2_100.txt │ ├── petMar2_36.txt │ ├── petMar2_50.txt │ ├── petMar2_75.txt │ ├── ponAbe2_100.txt │ ├── ponAbe2_36.txt │ ├── ponAbe2_50.txt │ ├── ponAbe2_75.txt │ ├── priPac1_100.txt │ ├── priPac1_36.txt │ ├── priPac1_50.txt │ ├── priPac1_75.txt │ ├── rheMac2_100.txt │ ├── rheMac2_36.txt │ ├── rheMac2_50.txt │ ├── rheMac2_75.txt │ ├── rheMac3_100.txt │ ├── rheMac3_36.txt │ ├── rheMac3_50.txt │ ├── rheMac3_75.txt │ ├── rheMac8_100.txt │ ├── rheMac8_36.txt │ ├── rheMac8_50.txt │ ├── rheMac8_75.txt │ ├── rhiRox1_100.txt │ ├── rhiRox1_36.txt │ ├── rhiRox1_50.txt │ ├── rhiRox1_75.txt │ ├── rn4_100.txt │ ├── rn4_36.txt │ ├── rn4_50.txt │ ├── rn4_75.txt │ ├── rn5_100.txt │ ├── rn5_36.txt │ ├── rn5_50.txt │ ├── rn5_75.txt │ ├── rn6_100.txt │ ├── rn6_36.txt │ ├── rn6_50.txt │ ├── rn6_75.txt │ ├── sacCer1_100.txt │ ├── sacCer1_36.txt │ ├── sacCer1_50.txt │ ├── sacCer1_75.txt │ ├── sacCer2_100.txt │ ├── sacCer2_36.txt │ ├── sacCer2_50.txt │ ├── sacCer2_75.txt │ ├── sacCer3_100.txt │ ├── sacCer3_36.txt │ ├── sacCer3_50.txt │ ├── sacCer3_75.txt │ ├── saiBol1_100.txt │ ├── saiBol1_36.txt │ ├── saiBol1_50.txt │ ├── saiBol1_75.txt │ ├── sorAra2_100.txt │ ├── sorAra2_36.txt │ ├── sorAra2_50.txt │ ├── sorAra2_75.txt │ ├── speTri2_100.txt │ ├── speTri2_36.txt │ ├── speTri2_50.txt │ ├── speTri2_75.txt │ ├── strPur1_100.txt │ ├── strPur1_36.txt │ ├── strPur1_50.txt │ ├── strPur1_75.txt │ ├── strPur2_100.txt │ ├── strPur2_36.txt │ ├── strPur2_50.txt │ ├── strPur2_75.txt │ ├── susScr2_100.txt │ ├── susScr2_36.txt │ ├── susScr2_50.txt │ ├── susScr2_75.txt │ ├── susScr3_100.txt │ ├── susScr3_36.txt │ ├── susScr3_50.txt │ ├── susScr3_75.txt │ ├── taeGut1_100.txt │ ├── taeGut1_36.txt │ ├── taeGut1_50.txt │ ├── taeGut1_75.txt │ ├── taeGut2_100.txt │ ├── taeGut2_36.txt │ ├── taeGut2_50.txt │ ├── taeGut2_75.txt │ ├── tarSyr2_100.txt │ ├── tarSyr2_36.txt │ ├── tarSyr2_50.txt │ ├── tarSyr2_75.txt │ ├── tetNig1_100.txt │ ├── tetNig1_36.txt │ ├── tetNig1_50.txt │ ├── tetNig1_75.txt │ ├── tetNig2_100.txt │ ├── tetNig2_36.txt │ ├── tetNig2_50.txt │ ├── tetNig2_75.txt │ ├── triMan1_100.txt │ ├── triMan1_36.txt │ ├── triMan1_50.txt │ ├── triMan1_75.txt │ ├── xenTro3_100.txt │ ├── xenTro3_36.txt │ ├── xenTro3_50.txt │ ├── xenTro3_75.txt │ ├── xenTro7_100.txt │ ├── xenTro7_36.txt │ ├── xenTro7_50.txt │ └── xenTro7_75.txt ├── examples │ ├── control.bed.gz │ └── test.bed.gz ├── main.py ├── src │ ├── SICER_stats.pyx │ ├── SICER_stats2.pyx │ ├── __init__.py │ ├── cpp_read_files.pxd │ ├── cpp_read_files.pyx │ ├── find_islands.pyx │ ├── genome_info.pyx │ ├── gzstream.cpp │ ├── gzstream.h │ ├── read_bam.pyx │ ├── read_files.cpp │ ├── reads_to_bins.pyx │ ├── remove_out_of_bounds_bins.py │ └── statistics.pyx └── version.py ├── examples ├── control.bam ├── control.bed ├── control.bed.gz ├── control.bedpe ├── control.bedpe.gz ├── control.sam ├── test.bam ├── test.bed ├── test.bed.gz ├── test.bedpe ├── test.bedpe.gz └── test.sam ├── graphs └── speed_epic2_vs_SICER_no_bigwig.png └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore-ntnu/epic2/HEAD/.gitignore -------------------------------------------------------------------------------- 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