├── FAQ.md ├── FragmentCut ├── DATA │ └── readme.md ├── code-110116.tar.gz └── readme.md ├── INSTALL ├── Makefile ├── README.md ├── UPDATES ├── hapcut-src ├── MECscore.c ├── Makefile ├── common.h ├── find_maxcut.c ├── find_starting_haplotypes.c ├── fragmatrix.c ├── fragmatrix.h ├── hapcut-annealing.c ├── hapcut.c ├── pointerheap.c ├── pointerheap.h ├── printhaplotypes.c ├── readinputfiles.c ├── readinputfiles.h └── removefalsehets.c ├── parsebam ├── Makefile ├── bamread.c ├── bamread.h ├── extracthairs.c ├── hapfragments.c ├── hapfragments.h ├── hashtable.c ├── hashtable.h ├── parsebamread.c ├── readfasta.c ├── readfasta.h ├── readvariant.c ├── readvariant.h └── samtools-0.1.18 │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog │ ├── INSTALL │ ├── Makefile │ ├── Makefile.mingw │ ├── NEWS │ ├── bam.c │ ├── bam.h │ ├── bam2bcf.c │ ├── bam2bcf.h │ ├── bam2bcf_indel.c │ ├── bam2depth.c │ ├── bam_aux.c │ ├── bam_cat.c │ ├── bam_color.c │ ├── bam_endian.h │ ├── bam_import.c │ ├── bam_index.c │ ├── bam_lpileup.c │ ├── bam_mate.c │ ├── bam_md.c │ ├── bam_pileup.c │ ├── bam_plcmd.c │ ├── bam_reheader.c │ ├── bam_rmdup.c │ ├── bam_rmdupse.c │ ├── bam_sort.c │ ├── bam_stat.c │ ├── bam_tview.c │ ├── bamtk.c │ ├── bcftools │ ├── Makefile │ ├── README │ ├── bcf.c │ ├── bcf.h │ ├── bcf.tex │ ├── bcf2qcall.c │ ├── bcfutils.c │ ├── call1.c │ ├── em.c │ ├── fet.c │ ├── index.c │ ├── kfunc.c │ ├── kmin.c │ ├── kmin.h │ ├── main.c │ ├── mut.c │ ├── prob1.c │ ├── prob1.h │ ├── vcf.c │ └── vcfutils.pl │ ├── bedidx.c │ ├── bgzf.c │ ├── bgzf.h │ ├── bgzip.c │ ├── cut_target.c │ ├── errmod.c │ ├── errmod.h │ ├── examples │ ├── 00README.txt │ ├── Makefile │ ├── bam2bed.c │ ├── calDepth.c │ ├── ex1.fa │ ├── ex1.sam.gz │ ├── toy.fa │ └── toy.sam │ ├── faidx.c │ ├── faidx.h │ ├── kaln.c │ ├── kaln.h │ ├── khash.h │ ├── klist.h │ ├── knetfile.c │ ├── knetfile.h │ ├── kprobaln.c │ ├── kprobaln.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.c │ ├── kstring.h │ ├── misc │ ├── HmmGlocal.java │ ├── Makefile │ ├── blast2sam.pl │ ├── bowtie2sam.pl │ ├── export2sam.pl │ ├── interpolate_sam.pl │ ├── maq2sam.c │ ├── md5.c │ ├── md5.h │ ├── md5fa.c │ ├── novo2sam.pl │ ├── psl2sam.pl │ ├── sam2vcf.pl │ ├── samtools.pl │ ├── seqtk.c │ ├── soap2sam.pl │ ├── varfilter.py │ ├── wgsim.c │ ├── wgsim_eval.pl │ └── zoom2sam.pl │ ├── phase.c │ ├── razf.c │ ├── razf.h │ ├── razip.c │ ├── sam.c │ ├── sam.h │ ├── sam_header.c │ ├── sam_header.h │ ├── sam_view.c │ ├── sample.c │ ├── sample.h │ ├── samtools.1 │ └── win32 │ ├── xcurses.h │ ├── zconf.h │ └── zlib.h ├── scripts ├── compare_hapcut_hairs.py ├── compare_hapcut_vcf.py ├── hap-simulation │ ├── README │ ├── YRI.1000genomes.chrom1.snplocs │ └── haplotypeassembly-simulator.c └── hapcutformat2vcf.py └── testdata ├── NA12878.chr20.1KG.vcf ├── NA18508.chr20.test.VCF ├── NA18508.chr20.test.bam ├── README.md └── fosmiddata.chr20.fragments /FAQ.md: -------------------------------------------------------------------------------- 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