├── GPL_3.0.txt ├── README.txt ├── RELEASE.txt ├── align.cpp ├── align.h ├── bsp2sam.py ├── dbseq.cpp ├── dbseq.h ├── debian ├── changelog ├── compat ├── control ├── copyright ├── postinst ├── prerm └── rules ├── main.cpp ├── makefile ├── methratio.py ├── pairs.cpp ├── pairs.h ├── param.cpp ├── param.h ├── reads.cpp ├── reads.h ├── sam2bam.sh ├── samtools ├── AUTHORS ├── COPYING ├── ChangeLog ├── INSTALL ├── Makefile ├── Makefile.mingw ├── NEWS ├── bam.c ├── bam.h ├── bam2bed.c ├── bam_aux.c ├── bam_color.c ├── bam_endian.h ├── bam_import.c ├── bam_index.c ├── bam_lpileup.c ├── bam_maqcns.c ├── bam_maqcns.h ├── bam_mate.c ├── bam_md.c ├── bam_pileup.c ├── bam_plcmd.c ├── bam_rmdup.c ├── bam_rmdupse.c ├── bam_sort.c ├── bam_stat.c ├── bam_tview.c ├── bamtk.c ├── bgzf.c ├── bgzf.h ├── bgzip.c ├── examples │ ├── 00README.txt │ ├── Makefile │ ├── calDepth.c │ ├── ex1.fa │ └── ex1.sam.gz ├── faidx.c ├── faidx.h ├── glf.c ├── glf.h ├── kaln.c ├── kaln.h ├── khash.h ├── klist.h ├── knetfile.c 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