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)
--
The Wellcome 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
