[Samtools-announce] [Samtools-devel] Release 1.5

[Valeriu O. <vo...@sa...>]

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.

------------------------------------------------------------------------------
samtools - changes v1.5
------------------------------------------------------------------------------

* 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).

------------------------------------------------------------------------------
BCFtools - changes v1.5
------------------------------------------------------------------------------

* 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


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