biology/fastp1.4.0

biology/fastp: Update to 1.4.0

Changelog: https://github.com/OpenGene/fastp/releases/tag/v1.4.0

Reviewed by:	jrm
Differential Revision:	https://reviews.freebsd.org/D60778

biology/fastp: Update to 1.2.0

Numerous improvements and fixes since 0.26.0
Changes: https://github.com/OpenGene/fastp/commits/master/

Reported by:    hayzam@alchemilla.io
Reviewed by:    jwb
Tested by:      jwb

biology/fastp: Update to 0.26.0

Improve adapter detection and trimming
Changes: https://github.com/OpenGene/fastp/releases
New maintainer: hayzam@alchemilla.io

Reported by:    portscout

biology/fastp: Update to 0.25.0

A few minor enhancements
Changes: https://github.com/OpenGene/fastp/commits/master/

Reported by:    portscout

biology/fastp: Update to 0.24.3

A couple bug fixes
Changes: https://github.com/OpenGene/fastp/releases

Reported by:    hayzam@alchemilla.io

biology/fastp: Update to 0.24.1

Bug fix release
Changes: https://github.com/OpenGene/fastp/releases

Reported by:    portscout

biology/fastp: Update to 0.24.0

Fix memory leaks
Changes: https://github.com/OpenGene/fastp/releases

Reported by:    portscout

biology/fastp: Update to 0.23.4

Fix regression in FASTQ reader
Changes: https://github.com/OpenGene/fastp/releases

Reported by:    portscout

biology/fastp: Update to 0.23.3

Fix hang on bad input and a few other bugs

Changes: https://github.com/OpenGene/fastp/releases

Reported by:    portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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/fastp: Add USE_GCC to hack around seg faults

Upstream has numerous open issues, so it's uncertain if or when the
issue with clang will be resolved.

biology/fastp: Update to 0.23.2

Interleaved input bug fix

biology/fastp: Update to 0.23.1

Performance improvements, more reproducible output
Fix seg fault when running with no args

biology/fastp: Update to 0.22.0

Add support for deduplication

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

Remove # $FreeBSD$ from Makefiles.

biology/fastp: Upgrade to 0.20.1

Fix the plotly.js CDN issue

Reported by:    portscout

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

biology/fastp: Remove redundant USE_GCC

biology/fastp: Respect WITH_DEBUG - do not strip binary

biology/fastp: Ultra-fast all-in-one FASTQ preprocessor

fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.