Noteworthy changes in release 1.3.1 (22 April 2016)
* Improved error checking and reporting, especially of I/O errors when
writing output files (#17, #315, PR #271, PR #317).
* Build fixes for 32-bit systems; be sure to run configure to enable
large file support and access to 2GiB+ files.
* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
Particular thanks to Kostya Kortchinsky of the Google Security Team
for testing and numerous input parsing bug reports.
* HTSlib now prints an informational message when initially creating a
CRAM reference cache in the default location under your $HOME directory.
(No message is printed if you are using $REF_CACHE to specify a location.)
* Avoided rare race condition when caching downloaded CRAM reference sequence
files, by using distinctive names for temporary files (in addition to O_EXCL,
which has always been used). Occasional corruption would previously occur
when multiple tools were simultaneously caching the same reference sequences
on an NFS filesystem that did not support O_EXCL (PR #320).
* Prevented race condition in file access plugin loading (PR #341).
* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
Continue anyway" warning messages (#299).
* Various minor CRAM fixes.
* Fixed documentation problems #348 and #358.
Noteworthy changes in release 1.3 (15 December 2015)
* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
and FTP, when HTSlib is configured to use libcurl for network file access
rather than the included basic knetfile networking.
* HTSlib can be built to use remote access hFILE backends (such as iRODS
and libcurl) via a plugin mechanism. This allows other backends to be
easily added and facilitates building tools that use HTSlib, as they
don't need to be linked with the backends' various required libraries.
* When writing CRAM output, sam_open() etc now default to writing CRAM v3.0
rather than v2.1.
* fai_build() and samtools faidx now accept initial whitespace in ">"
headers (e.g., "> chr1 description" is taken to refer to "chr1").
* tabix --only-header works again (was broken in 1.2.x; #249).
* HTSlib's configure script and Makefile now fully support the standard
convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
as needed. Previously the Makefile listened to $(LDLIBS) instead; if you
were overriding that, you should now override LIBS rather than LDLIBS.
* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
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