Samtools (and HTSlib) version 1.7 is now available from GitHub and SourceForge.
https://sourceforge.net/projects/samtools/
https://github.com/samtools/htslib/releases/tag/1.7
https://github.com/samtools/samtools/releases/tag/1.7
BCFtools 1.7 will follow soon.
The main changes are listed below:
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htslib - changes v1.7
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* BAM: HTSlib now supports BAMs which include CIGARs with more than
65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).
* BCF/VCF:
- Removed the need for long double in pileup calculations.
- Sped up the synced reader in some situations.
- Bug fixing: removed memory leak in bcf_copy.
* CRAM:
- Added support for HTS_IDX_START in cram iterators.
- Easier to build when lzma header files are absent.
- Bug fixing: a region query with REQUIRED_FIELDS option to
disable sequence retrieval now gives correct results.
- Bug fixing: stop queries to regions starting after the last
read on a chromosome from incorrectly reporting errors
(#651, #653; reported by Imran Haque and @egafni via pysam).
* Multi-region iterator: The new structure takes a list of regions and
iterates over all, deduplicating reads in the process, and producing a
full list of file offset intervals. This is usually much faster than
repeatedly using the old single-region iterator on a series of regions.
* Curl improvements:
- Add Bearer token support via HTS_AUTH_LOCATION env (#600).
- Use CURL_CA_BUNDLE environment variable to override the CA (#622;
thanks to Garret Kelly & David Alexander).
- Speed up (removal of excessive waiting) for both http(s) and ftp.
- Avoid repeatedly reconnecting by removal of unnecessary seeks.
- Bug fixing: double free when libcurl_open fails.
* BGZF block caching, if enabled, now performs far better (#629; reported
by Ram Yalamanchili).
* Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas
Hickman).
* Tidied up the drand48 support (intended for systems that do not
provide this function).
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samtools - changes v1.7
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* HTSlib, and so samtools, now support BAMs which include CIGARs with more
than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).
* samtools quickcheck will now write a warning to stderr if it finds
any problems. These messages can be suppressed with a new `-q` option.
* samtools markdup can now mark supplementary alignments of reads where
the primary alignment is found to be a duplicate. Supplementary marking
can be turned on by passing the `-S` option to markdup. When this
option is enabled, all the alignment data will be written to a temporary
file so that supplementary alignments that occur before a duplicated
primary can be correctly marked in the final output. The location
of this temporary file can be influenced using the new `-T` option.
* samtools view now supports HTSlib's new multi-region iterator.
This can be enabled by passing the `-M` option to view. When using
this option:
- The BED filter (`-L` option) will use the index to skip through the file
- Reads from overlapping regions will only be output once
* samtools bedcov will now ignore BED comment and header lines (#571; thanks
to Daniel Baker).
* samtools collate now updates the @HD SO: and GO: tags, and sort will
remove a GO: tag if present. (#757; reported by Imran Haque).
* Bug-fixes:
- maq2sam now checks for input files that end early. (#751; patch supplied
by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.)
- Fixed incorrect check when looking up header tags that could lead
to a crash in samtools stats. (#208; thanks to Dave Larson.)
- Fixed bug in samtools fastq `-O` option where it would fail if
the OQ tag in the input file had an unexpected type. (#758;
reported by Taejeong Bae)
- The MD5 calculations in samtools dict and md5fa did not handle
non-alphabetic characters in the same way as the CRAM MD5 function.
They have now been updated to match. (#704; reported by Chris Norman).
- Fix possible infinite loop in samtools targetcut.
- Building bam_tview_curses should no longer fail if a curses header file
cannot be found.
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 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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