[Samtools-help] HTSlib 1.3.2 released

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

A new 1.3.2 version of HTSlib has been released.  This is a very small increment over 1.3.1 that has been made to address two issues.

When converting directly from CRAM to BAM, for example with `samtools view -b foo.cram`, the bin field of a small fraction of the reads was previously calculated incorrectly.  This field is mostly unused so there was no effect on sequencing data, but it caused a validation error when such files were processed with Picard [1].

To work around this, you can use existing samtools to convert indirectly, e.g. with `samtools view -h foo.cram | samtools view -b`, or rebuild the existing samtools release against HTSlib 1.3.2 (by configuring --with-htslib=path/to/htslib-1.3.2), which fixes the problem.

The second issue is a minor file access plugin technicality that affects only those using the iRODS 4.1.x plugin or similar plugins.  With HTSlib 1.3.2, you no longer need to use the wrapper from <https://github.com/samtools/htslib-plugins>.

This release can be found at <http://www.htslib.org/>.  Development and source code are linked from that web site and can be found in various Git repositories under <https://github.com/samtools>.  Release archives are available at both GitHub and SourceForge.

    John

[1] See https://github.com/samtools/samtools/issues/574

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