Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtoolsReading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlibA C library for reading/writing high-throughput sequencing data
Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.
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File list (Check if you may need any files):
samtools-1.3.1\aclocal.m4
..............\AUTHORS
..............\bam.c
..............\bam.h
..............\bam2bcf.c
..............\bam2bcf.h
..............\bam2bcf_indel.c
..............\bam2depth.c
..............\bamshuf.c
..............\bamtk.c
..............\bam_addrprg.c
..............\bam_aux.c
..............\bam_cat.c
..............\bam_color.c
..............\bam_endian.h
..............\bam_flags.c
..............\bam_import.c
..............\bam_index.c
..............\bam_lpileup.c
..............\bam_lpileup.h
..............\bam_mate.c
..............\bam_md.c
..............\bam_plbuf.c
..............\bam_plbuf.h
..............\bam_plcmd.c
..............\bam_quickcheck.c
..............\bam_reheader.c
..............\bam_rmdup.c
..............\bam_rmdupse.c
..............\bam_sort.c
..............\bam_split.c
..............\bam_stat.c
..............\bam_tview.c
..............\bam_tview.h
..............\bam_tview_curses.c
..............\bam_tview_html.c
..............\bedcov.c
..............\bedidx.c
..............\ChangeLog.old
..............\config.h.in
..............\config.mk.in
..............\configure
..............\configure.ac
..............\cut_target.c
..............\dict.c
..............\errmod.c
..............\errmod.h
..............\.xamples\00README.txt
..............\........\ex1.fa
..............\........\ex1.sam.gz
..............\........\toy.fa
..............\........\toy.sam
..............\faidx.c
..............\htslib-1.3.1\bgzf.c
..............\............\bgzip.c
..............\............\config.h.in
..............\............\config.mk.in
..............\............\configure
..............\............\configure.ac
..............\............\.ram\cram.h
..............\............\....\cram_codecs.c
..............\............\....\cram_codecs.h
..............\............\....\cram_decode.c
..............\............\....\cram_decode.h
..............\............\....\cram_encode.c
..............\............\....\cram_encode.h
..............\............\....\cram_external.c
..............\............\....\cram_index.c
..............\............\....\cram_index.h
..............\............\....\cram_io.c
..............\............\....\cram_io.h
..............\............\....\cram_samtools.c
..............\............\....\cram_samtools.h
..............\............\....\cram_stats.c
..............\............\....\cram_stats.h
..............\............\....\cram_structs.h
..............\............\....\files.c
..............\............\....\mFILE.c
..............\............\....\mFILE.h
..............\............\....\misc.h
..............\............\....\open_trace_file.c
..............\............\....\open_trace_file.h
..............\............\....\os.h
..............\............\....\pooled_alloc.c
..............\............\....\pooled_alloc.h
..............\............\....\rANS_byte.h
..............\............\....\rANS_static.c
..............\............\....\rANS_static.h
..............\............\....\sam_header.c
..............\............\....\sam_header.h
..............\............\....\string_alloc.c
..............\............\....\string_alloc.h
..............\............\....\thread_pool.c
..............\............\....\thread_pool.h
..............\............\....\vlen.c
..............\............\....\vlen.h
..............\............\....\zfio.c
..............\............\....\zfio.h
..............\............\faidx.5
..............\............\faidx.c
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