[Bug 230170] biology/htslib: Update 1.9

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230170

            Bug ID: 230170
           Summary: biology/htslib: Update 1.9
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: Individual Port(s)
          Assignee: ports-bugs at FreeBSD.org
          Reporter: ndowens.fbsd at yandex.com
                CC: cartwright at asu.edu
                CC: cartwright at asu.edu
             Flags: maintainer-feedback?(cartwright at asu.edu)

Created attachment 195615
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=195615&action=edit
Update

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)

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