├── README.md ├── examples ├── data_files │ ├── 1S110_sorted.bam │ ├── 1S110_sorted.bam.bai │ ├── 1S111_sorted.bam │ ├── 1S111_sorted.bam.bai │ ├── 1S112_sorted.bam │ └── 1S112_sorted.bam.bai └── filenames.txt ├── external └── samtools │ ├── .gitignore │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog.old │ ├── INSTALL │ ├── Makefile │ ├── Makefile.mingw │ ├── NEWS │ ├── bam.c │ ├── bam.h │ ├── 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 │ ├── bam_tview.h │ ├── bam_tview_curses.c │ ├── bam_tview_html.c │ ├── bamshuf.c │ ├── bamtk.c │ ├── bcftools │ ├── Makefile │ ├── README │ ├── bcf.c │ ├── bcf.h │ ├── 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 │ ├── bedcov.c │ ├── bedidx.c │ ├── bgzf.c │ ├── bgzf.h │ ├── bgzip.c │ ├── cut_target.c │ ├── errmod.c │ ├── errmod.h │ ├── examples │ ├── 00README.txt │ ├── Makefile │ ├── bam2bed.c │ ├── calDepth.c │ ├── chk_indel.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 │ ├── ace2sam.c │ ├── bamcheck.c │ ├── blast2sam.pl │ ├── bowtie2sam.pl │ ├── export2sam.pl │ ├── interpolate_sam.pl │ ├── maq2sam.c │ ├── md5.c │ ├── md5.h │ ├── md5fa.c │ ├── novo2sam.pl │ ├── plot-bamcheck │ ├── psl2sam.pl │ ├── r2plot.lua │ ├── sam2vcf.pl │ ├── samtools.pl │ ├── 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