├── .gitmodules ├── .travis.yml ├── LICENSE.md ├── Makefile ├── README.md ├── RELEASE.md ├── VCF2R ├── benchmarking ├── CHM1 │ ├── truth_delly.pl │ ├── truth_lumpy.pl │ └── truth_wham.pl ├── PHASE3-1KG │ ├── README │ ├── comp_truth_delly1kg.pl │ ├── comp_truth_lumpy1kg.pl │ ├── comp_truth_wham1kg.pl │ └── estd214_1000_Genomes_Consortium_Phase_3.2014-10-13.GRCh37.p4.Submitted.NA12878.bedpe └── SIMULATED-DATA │ ├── truth_delly.pl │ ├── truth_lumpy.pl │ └── truth_wham.pl ├── data ├── LCR-hs37d5.bed ├── README └── WHAM_training_data.txt ├── docs ├── github-figure.ai ├── github-figure.png ├── wg.png ├── whamg_total_support.pdf ├── whamg_total_support_png.pdf └── whamg_total_support_png.png ├── src ├── bin │ ├── mergeIndv.cpp │ ├── wham.cpp │ └── whamg.cpp ├── doxygen-info │ └── Doxyfile ├── lib │ ├── JenksBreaks.h │ ├── KMERUTILS.h │ ├── alignHMM.h │ ├── cigar.hpp │ ├── dataStructures.hpp │ ├── entropy.cpp │ ├── entropy.h │ ├── fastonebigheader.h │ ├── flag.cpp │ ├── flag.h │ ├── gauss.c │ ├── gauss.h │ ├── gsl_cdf.h │ ├── gsl_math.h │ ├── join.hpp │ ├── phredUtils.h │ ├── readPileUp.cpp │ ├── readPileUp.h │ ├── read_pileup.cpp │ ├── read_pileup.h │ ├── split.cpp │ ├── split.h │ ├── ssw.c │ └── stats.hpp └── obj │ └── dummy ├── utils ├── README ├── Snakefile ├── classify_WHAM_vcf.py ├── dellyToBedPe.pl ├── deltaAfWham ├── filtWhamG.pl ├── gvfToBedPe.pl ├── whamToBed.pl └── whamToBedPe.pl └── whamg_total_support_png.pdf /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/.gitmodules -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/LICENSE.md -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/README.md -------------------------------------------------------------------------------- /RELEASE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/RELEASE.md -------------------------------------------------------------------------------- /VCF2R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/VCF2R -------------------------------------------------------------------------------- /benchmarking/CHM1/truth_delly.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/CHM1/truth_delly.pl -------------------------------------------------------------------------------- /benchmarking/CHM1/truth_lumpy.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/CHM1/truth_lumpy.pl -------------------------------------------------------------------------------- /benchmarking/CHM1/truth_wham.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/CHM1/truth_wham.pl -------------------------------------------------------------------------------- /benchmarking/PHASE3-1KG/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/PHASE3-1KG/README -------------------------------------------------------------------------------- /benchmarking/PHASE3-1KG/comp_truth_delly1kg.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/PHASE3-1KG/comp_truth_delly1kg.pl -------------------------------------------------------------------------------- /benchmarking/PHASE3-1KG/comp_truth_lumpy1kg.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/PHASE3-1KG/comp_truth_lumpy1kg.pl -------------------------------------------------------------------------------- /benchmarking/PHASE3-1KG/comp_truth_wham1kg.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/PHASE3-1KG/comp_truth_wham1kg.pl -------------------------------------------------------------------------------- /benchmarking/PHASE3-1KG/estd214_1000_Genomes_Consortium_Phase_3.2014-10-13.GRCh37.p4.Submitted.NA12878.bedpe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/PHASE3-1KG/estd214_1000_Genomes_Consortium_Phase_3.2014-10-13.GRCh37.p4.Submitted.NA12878.bedpe -------------------------------------------------------------------------------- /benchmarking/SIMULATED-DATA/truth_delly.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/SIMULATED-DATA/truth_delly.pl -------------------------------------------------------------------------------- /benchmarking/SIMULATED-DATA/truth_lumpy.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/SIMULATED-DATA/truth_lumpy.pl -------------------------------------------------------------------------------- /benchmarking/SIMULATED-DATA/truth_wham.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/benchmarking/SIMULATED-DATA/truth_wham.pl -------------------------------------------------------------------------------- /data/LCR-hs37d5.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/data/LCR-hs37d5.bed -------------------------------------------------------------------------------- /data/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/data/README -------------------------------------------------------------------------------- /data/WHAM_training_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/data/WHAM_training_data.txt -------------------------------------------------------------------------------- /docs/github-figure.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/github-figure.ai -------------------------------------------------------------------------------- /docs/github-figure.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/github-figure.png -------------------------------------------------------------------------------- /docs/wg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/wg.png -------------------------------------------------------------------------------- /docs/whamg_total_support.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/whamg_total_support.pdf -------------------------------------------------------------------------------- /docs/whamg_total_support_png.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/whamg_total_support_png.pdf -------------------------------------------------------------------------------- /docs/whamg_total_support_png.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/docs/whamg_total_support_png.png -------------------------------------------------------------------------------- /src/bin/mergeIndv.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/bin/mergeIndv.cpp -------------------------------------------------------------------------------- /src/bin/wham.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/bin/wham.cpp -------------------------------------------------------------------------------- /src/bin/whamg.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/bin/whamg.cpp -------------------------------------------------------------------------------- /src/doxygen-info/Doxyfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/doxygen-info/Doxyfile -------------------------------------------------------------------------------- /src/lib/JenksBreaks.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/JenksBreaks.h -------------------------------------------------------------------------------- /src/lib/KMERUTILS.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/KMERUTILS.h -------------------------------------------------------------------------------- /src/lib/alignHMM.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/alignHMM.h -------------------------------------------------------------------------------- /src/lib/cigar.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/cigar.hpp -------------------------------------------------------------------------------- /src/lib/dataStructures.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/dataStructures.hpp -------------------------------------------------------------------------------- /src/lib/entropy.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/entropy.cpp -------------------------------------------------------------------------------- /src/lib/entropy.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/entropy.h -------------------------------------------------------------------------------- /src/lib/fastonebigheader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/fastonebigheader.h -------------------------------------------------------------------------------- /src/lib/flag.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/flag.cpp -------------------------------------------------------------------------------- /src/lib/flag.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/flag.h -------------------------------------------------------------------------------- /src/lib/gauss.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/gauss.c -------------------------------------------------------------------------------- /src/lib/gauss.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/gauss.h -------------------------------------------------------------------------------- /src/lib/gsl_cdf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/gsl_cdf.h -------------------------------------------------------------------------------- /src/lib/gsl_math.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/gsl_math.h -------------------------------------------------------------------------------- /src/lib/join.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/join.hpp -------------------------------------------------------------------------------- /src/lib/phredUtils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/phredUtils.h -------------------------------------------------------------------------------- /src/lib/readPileUp.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/readPileUp.cpp -------------------------------------------------------------------------------- /src/lib/readPileUp.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/readPileUp.h -------------------------------------------------------------------------------- /src/lib/read_pileup.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/read_pileup.cpp -------------------------------------------------------------------------------- /src/lib/read_pileup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/read_pileup.h -------------------------------------------------------------------------------- /src/lib/split.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/split.cpp -------------------------------------------------------------------------------- /src/lib/split.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/split.h -------------------------------------------------------------------------------- /src/lib/ssw.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/ssw.c -------------------------------------------------------------------------------- /src/lib/stats.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/src/lib/stats.hpp -------------------------------------------------------------------------------- /src/obj/dummy: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /utils/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/README -------------------------------------------------------------------------------- /utils/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/Snakefile -------------------------------------------------------------------------------- /utils/classify_WHAM_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/classify_WHAM_vcf.py -------------------------------------------------------------------------------- /utils/dellyToBedPe.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/dellyToBedPe.pl -------------------------------------------------------------------------------- /utils/deltaAfWham: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/deltaAfWham -------------------------------------------------------------------------------- /utils/filtWhamG.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/filtWhamG.pl -------------------------------------------------------------------------------- /utils/gvfToBedPe.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/gvfToBedPe.pl -------------------------------------------------------------------------------- /utils/whamToBed.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/whamToBed.pl -------------------------------------------------------------------------------- /utils/whamToBedPe.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/utils/whamToBedPe.pl -------------------------------------------------------------------------------- /whamg_total_support_png.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/wham/HEAD/whamg_total_support_png.pdf --------------------------------------------------------------------------------