biology/ad2vcf 0.1.6.19

biology/ad2vcf: Update to 0.1.6.19

Use xt_fopen() to support all common compression tools
A few other minor improvements

biology/ad2vcf: Move man pages to share/man

Approved by:	portmgr (blanket)

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology/ad2vcf: Update to 0.1.6

Updates for bl_sam_t and bl_vcf_t API streamlining

Changes:        https://github.com/auerlab/ad2vcf/tags

biology/ad2vcf: Update to 0.1.5

Minor update for bioloibc 0.2.2 API changes

biology/ad2vcf: Update to 0.1.4

Updates for evolving libxtend and biolibc APIs
Add --version flag
Filter out unused SAM fields on input
Numerous other minor fixes and enhancements

Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4

biology/ad2vcf: Update to 0.1.3.31

Updates for libxtend and biolibc API changes
Clean up and minor bug fixes

biology/ad2vcf: Remove comment used to silence portlint

biology/ad2vcf: Update to 0.1.3

Updates for new biolibc API

Changes:        https://github.com/auerlab/ad2vcf/releases

One more small cleanup, forgotten yesterday. Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file

ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.