├── .gitignore ├── .gitmodules ├── .travis.yml ├── 1KG_Index ├── 1KG_IDs.txt ├── 1kG_ethnic_index.py └── README ├── LICENSE ├── Makefile ├── README.md ├── bin ├── plotBfst.R ├── plotHapLrt.R ├── plotHaplotypes.R ├── plotPfst.R ├── plotSmoothed.R ├── plotWCfst.R ├── plotXPEHH.R ├── plot_roc.r ├── vcf2sqlite.py ├── vcf_strip_extra_headers ├── vcfbiallelic ├── vcfclearid ├── vcfclearinfo ├── vcfcomplex ├── vcfgtcompare.sh ├── vcfindelproximity ├── vcfindels ├── vcfmultiallelic ├── vcfmultiway ├── vcfmultiwayscripts ├── vcfnobiallelicsnps ├── vcfnoindels ├── vcfnosnps ├── vcfnulldotslashdot ├── vcfplotaltdiscrepancy.r ├── vcfplotaltdiscrepancy.sh ├── vcfplotsitediscrepancy.r ├── vcfplottstv.sh ├── vcfprintaltdiscrepancy.r ├── vcfprintaltdiscrepancy.sh ├── vcfqualfilter ├── vcfregionreduce ├── vcfregionreduce_and_cut ├── vcfregionreduce_pipe ├── vcfregionreduce_uncompressed ├── vcfremovenonATGC ├── vcfsnps ├── vcfsort └── vcfvarstats ├── examples ├── 612.bFst_SatApr12_12_29_17.png ├── 612.counts_FriApr11_13_16_42.png ├── 612.nocounts.smoothed_TueApr15_13_25_53.png ├── 612.nocounts_FriApr11_13_16_38.png ├── 612.wcfst.txt_FriApr11_13_17_02.png ├── headCrest.haps.txt_ThuMay29_15_08_53.pdf ├── headCrest.haps.txt_ThuMay29_15_08_53.png ├── phasing-diff-res.png ├── phasing-results.png ├── scaffold612.d-stat.10kb.txt_abba-baba_WedOct29_10_17_10.png ├── t.hapass.txt_TueJun24_11_52_08.png ├── xp-phased.txt ├── xp-phased.txt_TueApr29_13_20_47.png ├── xp-unphased.txt ├── xp-unphased.txt_TueApr29_13_20_58.png └── xpehh_WedApr23_11_30_10.png ├── logos ├── websiteLogo.pdf └── websiteLogo.png ├── samples ├── sample.vcf ├── scaffold612.phased.vcf └── scaffold612.vcf └── src ├── BedReader.h ├── LD.cpp ├── Variant.cpp ├── Variant.h ├── abba-baba.cpp ├── bFst.cpp ├── cdflib.cpp ├── cdflib.hpp ├── convert.h ├── dumpContigsFromHeader.cpp ├── genotypeSummary.cpp ├── gl-XPEHH.cpp ├── gpatInfo.hpp ├── hapLrt.cpp ├── iHS.cpp ├── join.h ├── mt19937ar.h ├── pFst.cpp ├── pdflib.cpp ├── pdflib.hpp ├── permuteGPAT++.cpp ├── permuteGPATsmoother.cpp ├── plotHaps.cpp ├── popStats.cpp ├── rnglib.cpp ├── rnglib.hpp ├── segmentFst.cpp ├── sequenceDiversity.cpp ├── smoother.cpp ├── split.cpp ├── split.h ├── ssw.c ├── ssw.h ├── ssw_cpp.cpp ├── ssw_cpp.h ├── var.cpp ├── var.hpp ├── vcf2fasta.cpp ├── vcf2tsv.cpp ├── vcfaddinfo.cpp ├── vcfafpath.cpp ├── vcfallelicprimitives.cpp ├── vcfaltcount.cpp ├── vcfannotate.cpp ├── vcfannotategenotypes.cpp ├── vcfbreakmulti.cpp ├── vcfcat.cpp ├── vcfcheck.cpp ├── vcfclassify.cpp ├── vcfcleancomplex.cpp ├── vcfcombine.cpp ├── vcfcommonsamples.cpp ├── vcfcountalleles.cpp ├── vcfcreatemulti.cpp ├── vcfdistance.cpp ├── vcfecho.cpp ├── vcfentropy.cpp ├── vcfevenregions.cpp ├── vcffilter.cpp ├── vcffixup.cpp ├── vcfflatten.cpp ├── vcfgeno2alleles.cpp ├── vcfgeno2haplo.cpp ├── vcfgenosamplenames.cpp ├── vcfgenosummarize.cpp ├── vcfgenotypecompare.cpp ├── vcfgenotypes.cpp ├── vcfglbound.cpp ├── vcfglxgt.cpp ├── vcfhetcount.cpp ├── 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