Samtools (and HTSlib and BCFtools) version 1.6 is now available from
GitHub and SourceForge
https://sourceforge.net/projects/samtools/
https://github.com/samtools/htslib/releases/tag/1.6
https://github.com/samtools/samtools/releases/tag/1.6
https://github.com/samtools/bcftools/releases/tag/1.6
The main changes are listed below:
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htslib - changes v1.6
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* Fixed bug where iterators on CRAM files did not propagate error return
values to the caller correctly. Thanks go to Chris Saunders.
* Overhauled Windows builds. Building with msys2/mingw64 now works
correctly and passes all tests.
* More improvements to logging output (thanks again to Anders Kaplan).
* Return codes from sam_read1() when reading cram have been made
consistent with those returned when reading sam/bam. Thanks to
Chris Saunders (#575).
* BGZF CRC32 checksums are now always verified.
* It's now possible to set nthreads = 1 for cram files.
* hfile_libcurl has been modified to make it thread-safe. It's also
better at handling web servers that do not honour byte range requests
when attempting to seek - it now sets errno to ESPIPE and keeps
the existing connection open so callers can revert to streaming mode
it they want to.
* hfile_s3 now recalculates access tokens if they have become stale. This
fixes a reported problem where authentication failed after a file
had been in use for more than 15 minutes.
* Fixed bug where remote index fetches would fail to notice errors when
writing files.
* bam_read1() now checks that the query sequence length derived from the
CIGAR alignment matches the sequence length in the BAM record.
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samtools - changes v1.6
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* Added new markdup sub-command and '-m' option for fixmate. Used
together, they allow duplicates to be marked and optionally removed.
This fixes a number of problems with the old 'rmdup' sub-command, for
example samtools issue #497. 'rmdup' is kept for backwards
compatibility but 'markdup' should be used in preference.
* Sort is now much better at keeping within the requested memory limit.
It should also be slightly faster and need fewer temporary files when
the file to be sorted does not fit in memory. (#593; thanks to Nathan
Weeks.)
* Sort no longer rewrites the header when merging from files. It can also
now merge from memory, so fewer temporary files need to be written and
it is better at sorting in parallel when everything fits in memory.
* Both sort and merge now resolve ties when merging based on the position
in the input file(s). This makes them fully stable for all ordering
options. (Previously position sort was stable, but name and by tag
sorts were not).
* New --output-qname option for mpileup.
* Support for building on Windows using msys2/mingw64 or cygwin has
been improved.
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BCFtools - changes v1.6
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* New `sort` command.
* New options added to the `consensus` command. Note that the
`-i,--iupac` option has been renamed to `-I, --iupac`, in favor of the
standard `-i, --include`.
* Filtering expressions (`-i/-e`): support for `GT=<type>` expressions and
for lists and ranges (#639) - see the man page for details.
* `csq`: relax some GFF3 parsing restrictions to enable using Ensembl
GFF3 files for plants (#667)
* `stats`: add further documentation to output stats files (#316) and
include haploid counts in per-sample output (#671).
* `plot-vcfstats`: further fixes for Python3 (@nsoranzo, #645, #666).
* `query` bugfix (#632)
* `+setGT` plugin: new option to set genotypes based on a two-tailed
binomial distribution test. Also, allow combining `-i/-e` with `-t q`.
* `mpileup`: fix typo (#636)
* `convert --gvcf2vcf` bugfix (#641)
* `+mendelian`: recognize some mendelian inconsistencies that were
being missed (@oronnavon, #660), also add support for multiallelic
sites and sex chromosomes.
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
--
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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