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NEWS
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NEWS
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Noteworthy changes in release 1.2.1 (3 February 2015)
* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
but briefly removed in 1.2. This function is deprecated and will be removed
in a future release -- you should use hts_detect_format() etc instead
Noteworthy changes in release 1.2 (2 February 2015)
* HTSlib now has a configure script which checks your build environment
and allows for selection of optional extras. See INSTALL for details
* By default, reference sequences are fetched from the EBI CRAM Reference
Registry and cached in your $HOME cache directory. This behaviour can
be controlled by setting REF_PATH and REF_CACHE enviroment variables
(see the samtools(1) man page for details)
* Numerous CRAM improvements:
- Support for CRAM v3.0, an upcoming revision to CRAM supporting
better compression and per-container checksums
- EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
- Non-standard values for PNEXT and TLEN fields are now preserved
- hts_set_fai_filename() now provides a reference file when encoding
- Generated read names are now numbered from 1, rather than being
labelled 'slice:record-in-slice'
- Multi-threading and speed improvements
* New htsfile command for identifying file formats, and corresponding
file format detection APIs
* New tabix --regions FILE, --targets FILE options for filtering via BED files
* Optional iRODS file access, disabled by default. Configure with --with-irods
to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
* All occurences of 2^29 in the source have been eliminated, so indexing
and querying against reference sequences larger than 512Mbp works (when
using CSI indices)
* Support for plain GZIP compression in various places
* VCF header editing speed improvements
* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
faidx_fetch_nseq() will be deprecated and removed [#156]
* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks