./biology/htslib, C library for high-throughput sequencing data formats

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Branch: CURRENT, Version: 1.9, Package name: htslib-1.9, Maintainer: bacon

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.


Required to run:
[www/curl]

Required to build:
[pkgtools/cwrappers]

Master sites:

SHA1: 21be5187203df30637dda2e1133cae2e833ef050
RMD160: 85d5211cc197931e73a0dc7ca0673426f2ff6d89
Filesize: 1151.229 KB

Version history: (Expand)


CVS history: (Expand)


   2018-11-06 11:24:14 by Adam Ciarcinski | Files touched by this commit (2) | Package updated
Log message:
htslib: updated to 1.9

1.9:
If ./configure fails, make will stop working until either configure is re-run \ 
successfully, or make distclean is used. This makes configuration failures more \ 
obvious.

The default SAM version has been changed to 1.6. This is in line with the latest \ 
version specification and indicates that HTSlib supports the CG tag used to \ 
store long CIGAR data in BAM format.

bgzip integrity check option '--test'

Faidx can now index fastq files as well as fasta. The fastq index adds an extra \ 
column to the .fai index which gives the offset to the quality values. New \ 
interfaces have been added to htslib/faidx.h to read the fastq index and \ 
retrieve the quality values. It is possible to open a fastq index as if fasta \ 
(only sequences will be returned), but not the other way round.

New API interfaces to add or update integer, float and array aux tags.

Add level=<number> option to hts_set_opt() to allow the compression level \ 
to be set. Setting level=0 enables uncompressed output.

Improved bgzip error reporting.

Better error reporting when CRAM reference files can't be opened.

Fixes to make tests work properly on Windows/MinGW - mainly to handle line \ 
ending differences.

Efficiency improvements:

Small speed-up for CRAM indexing.

Reduce the number of unnecessary wake-ups in the thread pool.

Avoid some memory copies when writing data, notably for uncompressed BGZF output.

Bug fixes:

Fix multi-region iterator bugs on CRAM files.

Fixed multi-region iterator bug that caused some reads to be skipped incorrectly \ 
when reading BAM files.

Fixed synced_bcf_reader() bug when reading contigs multiple times.

Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when \ 
removing samples.

Fixed bug where the VCF record ref length was calculated incorrectly if an INFO \ 
END tag was present. (71b00a)

Fixed warnings found when compiling with gcc 8.1.0.

sam_hdr_read() and sam_hdr_write() will now return an error code if passed a \ 
NULL file pointer, instead of crashing.

Fixed possible negative array look-up in sam_parse1() that somehow escaped \ 
previous fuzz testing.

Fixed bug where cram range queries could incorrectly report an error when using \ 
multiple threads.

Fixed very rare rANS normalisation bug that could cause an assertion failure \ 
when writing CRAM files.
   2018-08-22 11:48:07 by Thomas Klausner | Files touched by this commit (3558)
Log message:
Recursive bump for perl5-5.28.0
   2018-07-04 15:40:45 by Jonathan Perkin | Files touched by this commit (423)
Log message:
*: Move SUBST_STAGE from post-patch to pre-configure

Performing substitutions during post-patch breaks tools such as mkpatches,
making it very difficult to regenerate correct patches after making changes,
and often leading to substituted string replacements being committed.
   2018-05-01 15:20:44 by Jason Bacon | Files touched by this commit (1)
Log message:
biology/htslib: Fix category in bl3
   2018-04-30 18:51:54 by Jason Bacon | Files touched by this commit (5)
Log message:
biology/htslib: import htslib-1.8

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.