23:21 Jason W. Bacon (jwb) 

biology/bio-mocha: Update to 1.16

New release to sync with bcftools

Changes: https://github.com/freeseek/mocha/commits/master

    09c70c7

21:10 Stefan Eßer (se) 

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)

    b7f0544

15:04 Jason W. Bacon (jwb) 

biology/bio-mocha: Update bcftools submodule to 1.15

Compatibility confirmed with upstream

    f46ddab

19:00 Jason W. Bacon (jwb) 

biology/bio-mocha: Update to 1.14-20220112

Upstream incorporated my patches to eliminate nested functions, which
are not standard C and pose security risks.
A few other minor updated.

    e33f720

16:17 Jason W. Bacon (jwb) 

bio-mocha: Build plugin against bcftools 1.14, the current port

    7a9f4b3

13:41 Jason W. Bacon (jwb) 

biology/bio-mocha: bcftools plugin for mosaic chromosomal alterations

MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.

    9152cfc