New 1.3 versions of Samtools, BCFtools, and HTSlib have been released. These
have numerous bug fixes, improvements, and new commands. The changes are too
numerous to list here, but we would particularly like to draw your attention to
these three items:
* The old way of invoking the samtools sort subcommand has been superseded
since samtools 1.0 and from this release no longer works:
samtools sort [-f] [-o] in.bam out.prefix
If you do use this obsolete way of specifying sort options, samtools will now
in most cases fail and give you a hint about the new ways. If you are still
using sort ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE
instead. See the manual page for details.
* The samtools rmdup command has been restored to its basic functionality. It
no longer immediately aborts, but it remains not recommended for most use.
* When HTSlib has been built to use libcurl, most tools can now access remote
files over HTTPS and via AWS S3 in addition to the previous HTTP, FTP, and
iRODS. See HTSlib's INSTALL and Samtools's README for details.
For further details of these and other changes in these releases, see the
release notes for each project linked to at <http://www.htslib.org/download/>,
or see all three together at
<http://sourceforge.net/projects/samtools/files/samtools/1.3/>.
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>. Release archives
are available at both GitHub and SourceForge.
Installing the tools will also install manual pages for them. Once installed,
you should be able to use "man samtools" etc at your command line to find
details of new commands and functionality. Manual pages and other
documentation are also available online at <http://www.htslib.org/doc/>.
John
--
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.
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