Dear all,
Samtools (and HTSlib and BCFtools) version 1.5 is now available from
github and sourceforge.
You can find the changes below:
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htslib - changes v1.5
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* Added a new logging API: hts_log(), along with hts_log_error(),
hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan for
the implementation. (#499, #543, #551)
* Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to alter
the hFILE buffer size.
* Fixed various bugs, including compilation issues
samtools/bcftools#610, samtools/bcftools#611 and robustness to corrupted
data #537, #538, #541, #546, #548, #549, #554.
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samtools - changes v1.5
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* Samtools fastq now has a -i option to create a fastq file from an
index tag, and a -T option (similar to -t) to add user specified aux
tags to the fastq header line.
* Samtools fastq can now create compressed fastq files, by giving the
output filenames an extention of .gq, .bgz, or .bgzf
* Samtools sort has a -t TAG option, that allows records to be sorted by
the value of the specified aux tag, then by position or name. Merge
gets a similar option, allowing files sorted this way to be merged.
(#675; thanks to Patrick Marks of 10xgenomics).
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BCFtools - changes v1.5
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* Added autoconf support to bcftools. See `INSTALL` for more details.
* `norm`: Make norm case insensitive (#601). Trim the reference allele
(#602).
* `mpileup`: fix for misreported indel depths for reads containing
adjacent indels (3c1205c1).
* `plot-vcfstats`: Open stats file in text mode, not binary (#618).
* `fixref` plugin: Allow multiallelic sites in the `-i, --use-id
reference`. Also flip genotypes, not just REF/ALT!
* `merge`: fix gVCF merge bug when last record on a chromosome opened a
gVCF block (#616)
* New options added to the ROH plotting script.
* `consensus`: Properly flush chain info (#606, thanks to @krooijers).
* New `+prune` plugin for pruning sites by LD (R2) or maximum number of
records within a window.
* New N_MISSING, F_MISSING (number and fraction missing) filtering
expressions.
* Fix HMM initialization in `roh` when snapshots are used in multiple
chromosome VCF.
* Fix buffer overflow (#607) in `filter`.
Best regards,
Valeriu
--
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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