[Bug 230171] biology/samtools: Update to 1.9

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230171

            Bug ID: 230171
           Summary: biology/samtools: Update to 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 195616
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=195616&action=edit
Update

Samtools mpileup VCF and BCF output is now deprecated. It is still functional,
but will warn. Please use bcftools mpileup instead. (#884)

    Samtools mpileup now handles the '-d' max_depth option differently. There
is no longer an enforced minimum, and '-d 0' is interpreted as limitless (no
maximum - warning this may be slow). The default per-file depth is now 8000,
which matches the value mpileup used to use when processing a single sample. To
get the previous default behaviour use the higher of 8000 divided by the number
of samples across all input files, or 250. (#859)

    Samtools stats new features:

        The '--remove-overlaps' option discounts overlapping portions of
templates when computing coverage and mapped base counting. (#855)

        When a target file is in use, the number of bases inside the target is
printed and the percentage of target bases with coverage above a given
threshold specified by the '--cov-threshold' option. (#855)

        Split base composition and length statistics by first and last reads.
(#814, #816)

    Samtools faidx new features:

        Now takes long options. (#509, thanks to Pierre Lindenbaum)

        Now warns about zero-length and truncated sequences due to the
requested range being beyond the end of the sequence. (#834)

        Gets a new option (--continue) that allows it to carry on when a
requested sequence was not in the index. (#834)

        It is now possible to supply the list of regions to output in a text
file using the new '--region-file' option. (#840)

        New '-i' option to make faidx return the reverse complement of the
regions requested. (#878)

        faidx now works on FASTQ (returning FASTA) and added a new fqidx
command to index and return FASTQ. (#852)

    Samtools collate now has a fast option '-f' that only operates on primary
pairs, dropping secondary and supplementary. It tries to write pairs to the
final output file as soon as both reads have been found. (#818)

    Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
reference skips (N) when computing coverage. (#843)

    Small speed up to samtools coordinate sort, by converting it to use radix
sort. (#835, thanks to Zhuravleva Aleksandra)

    Samtools idxstats now works on SAM and CRAM files, however this isn't fast
due to some information lacking from indices. (#832)

    Compression levels may now be specified with the level=N output-fmt-option.
E.g. with -O bam,level=3.

    Various documentation improvements.

    Bug-fixes:

        Improved error reporting in several places. (#827, #834, #877, cd7197)

        Various test improvements.

        Fixed failures in the multi-region iterator (view -M) when regions
provided via BED files include overlaps (#819, reported by Dave Larson).

        Samtools stats now counts '=' and 'X' CIGAR operators when counting
mapped bases. (#855)

        Samtools stats has fixes for insert size filtering (-m, -i). (#845;
#697 reported by Soumitra Pal)

        Samtools stats -F now longer negates an earlier -d option. (#830)

        Fix samtools stats crash when using a target region. (#875, reported by
John Marshall)

        Samtools sort now keeps to a single thread when the -@ option is
absent. Previously it would spawn a writer thread, which could cause the CPU
usage to go slightly over 100%. (#833, reported by Matthias Bernt)

        Fixed samtools phase '-A' option which was incorrectly defined to take
a parameter. (#850; #846 reported by Dianne Velasco)

        Fixed compilation problems when using C_INCLUDE_PATH. (#870; #817
reported by Robert Boissy)

        Fixed --version when built from a Git repository. (#844, thanks to John
Marshall)

        Use noenhanced mode for title in plot-bamstats. Prevents unwanted
interpretation of characters like underscore in gnuplot version 5. (#829,
thanks to M. Zapukhlyak)

        blast2sam.pl now reports perfect match hits (no indels or mismatches).
(#873, thanks to Nils Homer)

        Fixed bug in fasta and fastq subcommands where stdout would not be
flushed correctly if the -0 option was used.

        Fixed invalid memory access in mpileup and depth on alignment records
where the sequence is absent.

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