[Samtools-devel] Release 1.15.1

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

Samtools (and HTSlib and BCFtools) version 1.15.1 is now available from
GitHub and SourceForge.  This fixes bugs found in the 1.15 release.

https://sourceforge.net/projects/samtools/
https://github.com/samtools/htslib/releases/tag/1.15.1
https://github.com/samtools/samtools/releases/tag/1.15.1
https://github.com/samtools/bcftools/releases/tag/1.15.1
The main changes are listed below:

------------------------------------------------------------------------------
htslib - changes v1.15.1
------------------------------------------------------------------------------

* Security fix: Fixed broken error reporting in the sam_cap_mapq() function,
   due to a missing hts_log() parameter.  Prior to this fix it was possible
   to abuse the log message format string by passing a specially crafted
   alignment record to this function. (PR#1406)

* HTSlib now uses libhtscodecs release 1.2.2.  This fixes a number of bugs
   where invalid compressed data could trigger usage of uninitialised values.
   (PR#1416)

* Fixed excessive memory used by multi-threaded SAM output on long reads.
   (Part of PR#1384)

* Fixed a bug where tabix would misinterpret region specifiers starting at
   position 0.  It will also now warn if the file being indexed is supposed to
   be 1-based but has positions less than or equal to 0. (PR#1411)

* The VCF header parser will now issue a warning if it finds an INFO
   header with Type=Flag but Number not equal to 0.  It will also ignore
   the incorrect Number so the flag can be used. (PR#1415)

------------------------------------------------------------------------------
samtools - changes v1.15.1
------------------------------------------------------------------------------

Bug fixes:

  * A bug which prevented the samtools view --region-file (and the equivalent
    -M -L <file>) options from working in version 1.15 has been fixed. (#1617)

  * Fixed a crash triggered by using the samtools view -c/--count and --unmap
    options together.  The --unmap option is now ignored in counting mode.
    (#1619)

Documentation:

  * The consensus command was missing from the main samtools.1 manual page. It
    has now been added. (#1603)

  * Corrected instructions for reproducing the samtools stats "raw total
    sequences" count using samtools view -c. (#1620; reported by @krukanna)

  * Improved manual page formatting.  (#1625; thanks to John Marshall)

Non user-visible changes and build improvements:

  * Unnecessary #include lines have been removed from bam_plcmd.c. (#1607;
    thanks to John Marshall)

------------------------------------------------------------------------------
bcftools - changes v1.15.1
------------------------------------------------------------------------------

* bcftools annotate

     - New `-H, --header-line` convenience option to pass a header line on
       command line, this complements the existing `-h, --header-lines` option
       which requires a file with header lines

* bcftools csq

     - A list of consequence types supported by `bcftools csq` has been added
       to the manual page. (#1671)

* bcftools +fill-tags

     - Extend generalized functions so that FORMAT tags can be filled as well,
       for example:

        bcftools +fill-tags in.bcf -o out.bcf -- \
            -t 'FORMAT/DP:1=int(smpl_sum(FORMAT/AD))'

     - Allow multiple custom functions in a single run. Previously the program
       would silently go with the last one, assigning the same values to all
       (#1684)

* bcftools norm

     - Fix an assertion failure triggered when a faulty VCF file with a '-'
       character in the REF allele was used with `bcftools norm --atomize`.
       This option now checks that the REF allele only includes the allowed
       characters A, C, G, T and N. (#1668)

     - Fix the loss of phasing in half-missing genotypes in variant
       atomization (#1689)

* bcftools roh

     - Fix a bug that could result in an endless loop or incorrect AF estimate
       when missing genotypes are present and the `--estimate-AF -` option was
       used (#1687)

* bcftools +split-vep

     - VEP fields with characters disallowed in VCF tag names by the
       specification (such as '-' in 'M-CAP') couldn't be queried. This
       has been fixed, the program now sanitizes the field names,
       replacing invalid characters with underscore (#1686)



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