- Update to version 1.16
* Make hfile_s3 refresh AWS credentials on expiry in order to make
HTSlib work better with AWS IAM credentials, which have a
limited lifespan.
* Allow BAM headers between 2GB and 4GB in size once more.
* Improve error message when failing to load an index.
* Permit MM (base modification) tags containing . and ? suffixes.
* Warn if spaces instead of tabs are detected in a VCF file to
prevent confusion.
* Add an sclen filter expression keyword.
* Improve error messages for CRAM reference mismatches.
* Expose more of the CRAM API and add new functionality to extract
the reference from a CRAM file.
* Improvements to the implementation of embedded references in CRAM
where no external reference is specified.
* The CRAM writer now allows alignment records with RG:Z: aux tags
that don't have a corresponding @RG ID in the file header.
* Set tab delimiter in man page for tabix GFF3 sort.
* When using libdeflate, the 1...9 scale of BGZF compression levels
is now remapped to the 1...12 range used by libdeflate instead of
being passed directly.
* The VCF variant API has been extended so that it can return separate
flags for INS and DEL variants as well as the existing INDEL one.
* The missing, but trivial, le_to_u8() function has been added
to hts_endian.
* bcf_format_gt() now works properly on big-endian platforms.
* Update htscodecs to version 1.3.0 for new SIMD code + various fixes.
* Detect ARM Neon support and only build appropriate SIMD object files.
* make print-config now reports extra CFLAGS that are needed to build
the SIMD parts of htscodecs.
* Fixed some Makefile dependency issues for the check/test targets
and plugins.
* Fix bug when reading position -1 in BCF (0 in VCF), which is used
to indicate telomeric regions.
* Various bugs and quirks have been fixed in the filter expression
engine, mostly related to the handling of absent tags, and
the is_true flag.
* Fix buffer overrun in bam_plp_insertion_mod.
* Remove limit of returned size from fai_retrieve().
* Cap hts_getline() return value at INT_MAX.
* Fix breakend detection and test bcf_set_variant_type().
* Prevent arrays of BCF_BT_NULL values found in BCF files from
causing bcf_fmt_array() to call exit() as the type is unsupported.
* Improved detection of fasta and fastq files that have very long
comments following identifiers.
* Fixed a SEGV triggered by giving a SAM file to samtools import.
OBS-URL: https://build.opensuse.org/request/show/1002209
OBS-URL: https://build.opensuse.org/package/show/science/libhts?expand=0&rev=15
- Update to release 1.10.2
* This is a release fix that corrects minor inconsistencies discovered in
previous deliverables.
- Update to release 1.10.1
* The support for 64-bit coordinates in VCF brought problems for files
not conforming to VCF/BCF specification. While previous versions would
make out-of-range values silently overflow creating nonsense values
but parseable file, the version 1.10 would silently create an invalid BCF.
- Update to release 1.10
+ Brief summary
* Addition of support for references longer than 2Gb (NB: SAM and VCF
formats only, not their binary counterparts). This may need changes
in code using HTSlib. See README.large_positions.md for more information.
* Added a SAM header API.
* Major speed up to SAM reading and writing. This also now supports
multi-threading.
* We can now auto-index on-the-fly while writing a file. This also
includes to bgzipped SAM.gz.
* Overhaul of the S3 interface, which now supports version 4
signatures. This also makes writing to S3 work.
OBS-URL: https://build.opensuse.org/request/show/770317
OBS-URL: https://build.opensuse.org/package/show/science/libhts?expand=0&rev=6
- Update to 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. (#711, thanks to John Marshall)
* 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' (#682, thanks to @sd4B75bJ, @jrayner)
* 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. (#701)
* New API interfaces to add or update integer, float and array aux tags. (#694)
* Add `level=<number>` option to `hts_set_opt()` to allow the compression
level to be set. Setting `level=0` enables uncompressed output. (#715)
* Improved bgzip error reporting.
* Better error reporting when CRAM reference files can't be opened. (#706)
* Fixes to make tests work properly on Windows/MinGW - mainly to handle
line ending differences. (#716)
* Efficiency improvements:
- Small speed-up for CRAM indexing.
- Reduce the number of unnecessary wake-ups in the thread pool. (#703)
- Avoid some memory copies when writing data, notably for uncompressed
BGZF output. (#703)
* Bug fixes:
- Fix multi-region iterator bugs on CRAM files. (#684)
- Fixed multi-region iterator bug that caused some reads to be skipped
incorrectly when reading BAM files. (#687)
- Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691,
reported by @freeseek)
- Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary
when removing samples. (#692, reported by @freeseek)
- 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. (#700)
- 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. (#731, reported by @fCorleone)
- Fixed bug where cram range queries could incorrectly report an error
when using multiple threads. (#734, reported by Brent Pedersen)
- Fixed very rare rANS normalisation bug that could cause an assertion
failure when writing CRAM files. (#739, reported by @carsonhh)
OBS-URL: https://build.opensuse.org/request/show/633580
OBS-URL: https://build.opensuse.org/package/show/science/libhts?expand=0&rev=5
