[Bug 230169] biology/bcftools: Update 1.9

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230169

            Bug ID: 230169
           Summary: biology/bcftools: 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
             Flags: maintainer-feedback?(cartwright at asu.edu)
                CC: cartwright at asu.edu

Created attachment 195614
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=195614&action=edit
Update

Release Notes:

    annotate

        REF and ALT columns can be now transferred from the annotation file.

        fixed bug when setting vector_end values.

    consensus

        new -M option to control output at missing genotypes

        variants immediately following insersions should not be skipped. Note
however, that the current fix requires normalized VCF and may still falsely
skip variants adjacent to multiallelic indels.

        bug fixed in -H selection handling

    convert

        the --tsv2vcf option now makes the missing genotypes diploid, "./."
instead of "."

        the behavior of -i/-e with --gvcf2vcf changed. Previously only sites
with FILTER set to "PASS" or "." were expanded and the -i/-e options dropped
sites completely. The new behavior is to let the -i/-e options control which
records will be expanded. In order to drop records completely, one can stream
through "bcftools view" first.

    csq

        since the real consequence of start/splice events are not known, the
aminoacid positions at subsequent variants should stay unchanged

        add --force option to skip malformatted transcripts in GFFs with
out-of-phase CDS exons.

    +dosage: output all alleles and all their dosages at multiallelic sites

    +fixref: fix serious bug in -m top conversion

    -i/-e filtering expressions:

        add two-tailed binomial test

        add functions N_PASS() and F_PASS()

        add support for lists of samples in filtering expressions, with many
samples it was impractical to list them all on the command line. Samples can be
now in a file as, e.g., GT[@samples.txt]="het"

        allow multiple perl functions in the expressions and some bug fixes

        fix a parsing problem, @ was not removed from @filename expressions

    mpileup: fixed bug where, if samples were renamed using the -G
(--read-groups) option, some samples could be omitted from the output file.

    norm: update INFO/END when normalizing indels

    +split: new -S option to subset samples and to use custom file names
instead of the defaults

    +smpl-stats: new plugin

    +trio-stats: new plugin

    Fixed build problems with non-functional configure script produced on some
platforms

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