[Samtools-announce] Release 1.8

[Robert D. <rm...@sa...>]

Samtools (and HTSlib and BCFtools) version 1.8 is now available from
GitHub and SourceForge

https://sourceforge.net/projects/samtools/

https://github.com/samtools/htslib/releases/tag/1.8
https://github.com/samtools/samtools/releases/tag/1.8
https://github.com/samtools/bcftools/releases/tag/1.8

The main changes are listed below:

------------------------------------------------------------------------------
htslib - changes v1.8
------------------------------------------------------------------------------

* The URL to get sequences from the EBI reference server has been changed to
   https://.  This is because the EBI no longer serve sequences via plain HTTP
   - requests to the http:// endpoint just get redirected. HTSlib needs to be
   linked against libcurl to download https:// URLs, so CRAM users who want to
   get references from the EBI will need to run configure and ensure libcurl
   support is enabled using the --enable-libcurl option.

* Added libdeflate as a build option for alternative faster compression and
   decompression.  Results vary by CPU but compression should be twice as fast
   and decompression faster.

* It is now possible to set the compression level in bgzip.  (#675; thanks to
   Nathan Weeks).

* bgzip now gets its own manual page.

* CRAM encoding now stored MD and NM tags verbatim where the reference
   contains 'N' characters, to work around ambiguities in the SAM
   specification (samtools #717/762). Also added "store_md" and "store_nm"
   cram-options for forcing these tags to be stored at all locations.
   This is best when combined with a subsequent decode_md=0 option while
   reading CRAM.

* Multiple CRAM bug fixes, including a fix to free and the subsequent reuse
   of references with `-T ref.fa`. (#654; reported by Chris Saunders)

* CRAM multi-threading bugs fixed: don't try to call flush on reading;
   processing of multiple range queries; problems with multi-slice containers.

* Fixed crashes caused when decoding some cramtools produced CRAM files.

* Fixed a couple of minor rANS issues with handling invalid data.

* Fixed bug where probaln_glocal() tried to allocate far more memory than
   needed when the query sequence was much longer than the reference.  This
   caused crashes in samtools and bcftools mpileup when used on data with very
   long reads. (#572, problem reported by Felix Bemm via minimap2).

* sam_prop_realn() now returns -1 (the same value as for unmapped reads) on
   reads that do not include at least one 'M', 'X' or '=' CIGAR operator,
   and no longer adds BQ or ZQ tags.  BAQ adjustments are only made to bases
   covered by these operators so there is no point in trying to align reads
   that do not have them. (#572)

------------------------------------------------------------------------------
samtools - changes v1.8
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  * samtools calmd now has a quiet mode.  This can be enabled by passing `-Q`
    to calmd. (Thanks to Colin Davenport)

  * In samtools depth `-d 0` will effectively remove the depth limit. (#764)

  * Improvements made to samtools collate's interface and documentation.
    It is now possible to specify an output file name using `-o`, instead
    of deriving it from the prefix used for temporary files.  The prefix
    itself is now optional if `-o` or `-O` (to stdout) is used. (#780)

  * Bug-fixes:

    - Make samtools addreplacerg choose output format by file extension.
      (#767; reported by Argy Megalios)

    - Merge tests now work on ungzipped data, allowing tests to be run against
      different deflate libraries.

    - samtools markdup error messages about missing tags have been updated
      with the suggestion that samtools fixmate is run beforehand. (#765;
      reported by Yudong Cai)

    - Enables the `--reference` option for samtools fastq.  Now works like
      other programs when a reference sequence is needed for CRAM files.
      (#791, reported by Milana Kaljevic)

------------------------------------------------------------------------------
bcftools - changes v1.8
------------------------------------------------------------------------------

* `-i, -e` filtering: Support for custom perl scripts

* `+contrast`: New plugin to annotate genotype differences between groups of
   samples

* `+fixploidy`: New options for simpler ploidy usage

* `+setGT`: Target genotypes can be set to phased by giving `--new-gt p`

* `run-roh.pl`: Allow to pass options directly to `bcftools roh`

* Number of bug fixes

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919


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