GitHub - benjschiller/samtools: Historical archive: old samtools fork for Windows/MSVC support for pysam-era workflows. Not maintained; use upstream.

This repository was archived by the owner on Jun 22, 2026. It is now read-only.

Name		Name	Last commit message	Last commit date
Latest commit History 298 Commits
bcftools		bcftools
math		math
misc		misc
win32		win32
.gitignore		.gitignore
AUTHORS		AUTHORS
COPYING		COPYING
ChangeLog		ChangeLog
ChangeLog.old		ChangeLog.old
INSTALL		INSTALL
Makefile		Makefile
Makefile.mingw		Makefile.mingw
NEWS		NEWS
README		README
bam.c		bam.c
bam.h		bam.h
bam2bcf.c		bam2bcf.c
bam2bcf.h		bam2bcf.h
bam2bcf_indel.c		bam2bcf_indel.c
bam2depth.c		bam2depth.c
bam_aux.c		bam_aux.c
bam_cat.c		bam_cat.c
bam_color.c		bam_color.c
bam_endian.h		bam_endian.h
bam_import.c		bam_import.c
bam_index.c		bam_index.c
bam_lpileup.c		bam_lpileup.c
bam_mate.c		bam_mate.c
bam_md.c		bam_md.c
bam_pileup.c		bam_pileup.c
bam_plcmd.c		bam_plcmd.c
bam_reheader.c		bam_reheader.c
bam_rmdup.c		bam_rmdup.c
bam_rmdupse.c		bam_rmdupse.c
bam_sort.c		bam_sort.c
bam_stat.c		bam_stat.c
bam_tview.c		bam_tview.c
bamtk.c		bamtk.c
bedidx.c		bedidx.c
bgzf.c		bgzf.c
bgzf.h		bgzf.h
bgzip.c		bgzip.c
cut_target.c		cut_target.c
errmod.c		errmod.c
errmod.h		errmod.h
faidx.c		faidx.c
faidx.h		faidx.h
kaln.c		kaln.c
kaln.h		kaln.h
khash.h		khash.h
klist.h		klist.h
knetfile.c		knetfile.c
knetfile.h		knetfile.h
kprobaln.c		kprobaln.c
kprobaln.h		kprobaln.h
kseq.h		kseq.h
ksort.h		ksort.h
kstring.c		kstring.c
kstring.h		kstring.h
msvc_compat.h		msvc_compat.h
phase.c		phase.c
razf.c		razf.c
razf.h		razf.h
razip.c		razip.c
sam.c		sam.c
sam.h		sam.h
sam_header.c		sam_header.c
sam_header.h		sam_header.h
sam_view.c		sam_view.c
sample.c		sample.c
sample.h		sample.h
samtools.1		samtools.1

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# Historical archive

This repository is a historical fork of samtools that was used to preserve
Windows / MSVC support work for pysam-era workflows.

It is not the official samtools repository and is no longer maintained. For
current samtools development, releases, documentation, and issue tracking, use
the upstream project instead:

https://www.htslib.org/
https://github.com/samtools/samtools