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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
