├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── README_msisensor.md ├── bampairs.cpp ├── bampairs.h ├── bamreader.cpp ├── bamreader.h ├── bamtumors.cpp ├── chi.cpp ├── chi.h ├── cmds.cpp ├── cmds.h ├── distribution.cpp ├── distribution.h ├── homo.cpp ├── homo.h ├── makefile ├── param.cpp ├── param.h ├── polyscan.cpp ├── polyscan.h ├── refseq.cpp ├── refseq.h ├── sample.cpp ├── sample.h ├── scan.cpp ├── scan.h ├── somatic.cpp ├── somatic.h ├── structs.h ├── test ├── all_CDS_and_ncRNA_24Chroms_Contigs_1BasedStart_2bpFlanks_ForMusic ├── example.bed ├── example.microsate.sites ├── example.normal.bam ├── example.normal.bam.bai ├── example.tumor.bam ├── example.tumor.bam.bai ├── msi_score_and_status_distribution.jpg ├── msi_score_and_status_distribution.pdf ├── msi_score_and_status_list ├── msi_score_only_distribution.jpg ├── msi_score_only_distribution.pdf ├── msi_score_only_list ├── msisensor-tumor-only.png ├── plot.r ├── run.sh └── tumor_only_vs_pair.jpg ├── utilities.cpp ├── utilities.h ├── vendor └── samtools-0.1.19 │ ├── .gitignore │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog.old │ ├── 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 │ ├── bam_tview.h │ ├── bam_tview_curses.c │ ├── bam_tview_html.c │ ├── bamshuf.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 │ ├── 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 │ ├── soap2sam.pl │ ├── varfilter.py │ ├── vcfutils.lua │ ├── wgsim.c │ ├── wgsim_eval.pl │ └── zoom2sam.pl │ ├── padding.c │ ├── phase.c │ ├── razf.c │ ├── razf.h │ ├── razip.c │ ├── sam.c │ ├── sam.h │ ├── sam_header.c │ ├── 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