SAM tools Files

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htslib - changes v1.15.1
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* 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)

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samtools - changes v1.15.1
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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)

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bcftools - changes v1.15.1
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* 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)