20:04 Nuno Teixeira (eduardo) 

biology/vcf-split: Move man pages to share/man

Approved by:	portmgr (blanket)

    0a569bf

11:41 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.5.10

Updates for new libxtend API

    1d29500

20:11 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.5-4

Update for biolibc API changes

    73209dc

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

14:26 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.5

Use stremalined biolibc API
Minor build system improvements

Changes:        https://github.com/auerlab/vcf-split/tags

    ef8583e

21:43 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.4

Minor update for biolibc 0.2.2 API changes

    58a9101

19:45 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.3.3

Transfer header from multi-sample input
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements

    300dbd1

01:30 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.2.14

Updates for libxtend and biolibc API changes

    61ebfe4

15:05 Jason W. Bacon (jwb) 

biology/vcf-split: Update to 0.1.2

Updates for new biolibc API

Changes:        https://github.com/auerlab/vcf-split/releases

    f2ef77c

08:09 Mathieu Arnold (mat) 

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

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

15:17 jwb 

biology/vcf-split: Split a multi-sample VCF into single-sample VCFs

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.