Log Message:
htslib: updated to 1.16

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. This is not permitted \ 
in the BAM specification but was allowed in an earlier version of HTSlib. There \ 
is now a warning at 2GB and a hard failure at 4GB.

Improve error message when failing to load an index.

Permit MM (base modification) tags containing . and ? suffixes. These define \ 
implicit vs explicit coordinates. See the SAM tags specification for details.

Warn if spaces instead of tabs are detected in a VCF file to prevent confusion.

Add an sclen filter expression keyword. This is the length of a soft-clip, both \ 
left and right end. It may be combined with qlen (qlen-sclen) to obtain the \ 
number of bases in the query sequence that have been aligned to the genome ie it \ 
provides a way to compare local-alignment vs global-alignment length.

Improve error messages for CRAM reference mismatches. If the user specifies the \ 
wrong reference, the CRAM slice header MD5sum checks fail. We now report the SQ \ 
line M5 string too so it is possible to validate against the whole chr in the \ 
ref.fa file. The error message has also been improved to report the reference \ 
name instead of #num. Finally, we now hint at the likely cause, which counters \ 
the misleading samtools supplied error of "truncated or corrupt" file.

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. Previously these tags would have been \ 
silently dropped. HTSlib will complain whenever it has to add one though, as \ 
such tags do not conform to recommended practice for the SAM, BAM and CRAM \ 
formats.

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. In particular, HTSlib levels 8 and 9 now map to libdeflate levels 10 \ 
and 12, so it is possible to select the highest (but slowest) compression \ 
offered by libdeflate.

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. These flags have not \ 
been added to the old bcf_get_variant_types() interface as it could break \ 
existing users. To access them, it is necessary to use new functions \ 
bcf_has_variant_type() and bcf_has_variant_types().

The missing, but trivial, le_to_u8() function has been added to hts_endian.

bcf_format_gt() now works properly on big-endian platforms.