SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments. The original samtools package has
been split into three separate but tightly coordinated projects: htslib
(C library for handling high-throughput sequencing data), samtools (for
handling SAM, BAM, CRAM), and bcftools (for handling VCF and BCF).
Samtools is now distributed as an individual package. Installation is
set up so that the code uses an external HTSlib (also at SBo). Although
deprecated upstream, in the case that people need parts of
samtools-legacy (e.g header files or libbam) these can be installed from
this package by modifying the samtools.Slackbuild. Note that the sam.h
of htslib differs from sam.h coming with samtools.
Prior to the introduction of HTSlib, SAMtools and BCFtools were
distributed in a single samtools-0.1.x package. This old version remains
available from SBo as samtools-legacy.
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