[Samtools-announce] samtools/bcftools/htslib 1.0 released

[John M. <jm...@sa...>]

Major new versions of samtools and associated tools have been released.  Significant changes include:

* support for CRAM, a sequence data file format with better compression than BAM
* support for BCF v2, a binary equivalent to the VCF format that is more flexible than the old BCF1
* bcftools has been split out from samtools as a fully-featured VCF/BCF manipulation toolkit
* much work on the variant calling algorithms
* replacement of samtools's SAM/BAM readers and writers with new implementations in htslib
* a more flexible API for writing programs using htslib's API rather than the old samtools bam.h (which will remain supported and usable for a while yet)

BCFtools has been significantly expanded to provide many tools for basic manipulation of VCF and BCF files.  Both SAMtools and BCFtools now use HTSlib for their low-level SAM/BAM/CRAM and VCF/BCF file operations.  Due to these reorganisations there are many small changes and improvements -- notably most tools automatically detect what kind of input files they have been provided with.

These releases can be found at <http://www.htslib.org/>.  Development and source code of these projects are linked from that web site and can be found in various Git repositories under <https://github.com/samtools>.  The web site at <http://samtools.sourceforge.net> contains information for the old 0.1.x samtools/bcftools releases which is still useful but needs some updating for the 1.0 release.

The <http://www.htslib.org/> website will be updated over the coming days and weeks with new workflows and updated information from the old website.  It has been a long time since the last samtools release -- we anticipate making more frequent samtools, bcftools, and htslib releases in future.

    John

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