biology/biolibc 0.2.7

biology/biolibc: Update to 0.2.7

Minor fixes and enhancements
Changes: https://github.com/auerlab/biolibc/releases

biology/biolibc: Update to 0.2.6.4

bl_sam_copy(): Make sure all fields are properly initialized

biology/biolibc: Impelled to share/man

Approved by:    portmgr (blanket)

biology/biolibc: Update to 0.2.6

Updates for libxtend 0.2.0 API
Add full list of functions to biolibc(3) man page
Other documentation improvements
Changes: https://github.com/auerlab/biolibc/releases

biology/biolibc: Update to 0.2.5

Make header files C++ compatible (extern C)
bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p
bl_gff_extract_attribute(): Improve performance
gff -> gff3 to distinguish from past and future GFF specs
Silence some compiler warnings

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

biology/biolibc: Update to 0.2.4.3

Add extern "C" to support use from C++ apps

biology/biolibc: Update to 0.2.4

Minor enhancements

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

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/biolibc: Update to 0.2.3

Expand use of tsv_read_field_malloc() to improve memory efficiency
Add SAM bit flag constants
Import SAM-GFF compare functions from diffanal
Updates for libxtend DSV API changes
Numerous minor bug fixes and enhancements

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

biology/biolibc: Update to 0.2.2

Numerous bug fixes and enhancements
Serveral new functions
3 new classes
Cleaned up some API slop
Changes: https://github.com/auerlab/biolibc/tags

biology/biolibc: Update to 0.2.1

Add orf.c with start/stop codon locators
Standardize BED and GFF APIs
Implement VCF input filtering
Eliminate mutator macros mirroring mutator functions
Numerous minor bug fixes and enhancements

Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1

biology/biolibc: Update to 0.2.0.11

Regenerate man pages with improved auto-c2man
Adds missing return value sections and improves formatting

biology/biolibc: Update to 0.2.0.1

Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks

biology/biolibc: Update to 0.2.0

Major API overhaul
New classes for FASTA and FASTQ
Generate accessor and mutator functions for all classes
Generate man pages for all functions and macros
Export delimiter-separated-value class to libxtend

biology/biolibc: Remove comment used to silence portlint

biology/biolibc: Update to 0.1.3

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

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

Remove # $FreeBSD$ from Makefiles.

biology/biolibc: Low-level high-performance bioinformatics library

Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data.  Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications.  These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.