- 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.