GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more. The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
*: Fix WWW with broken anchors-as-comments
Case 1: WWW=https://example.com#foo
Here #foo is not part of the value of WWW since # introduces a comment
whether it's part of a word or not (quoting the word+# makes no
difference either). # needs to be escaped:
WWW=https://example.com\#foo
Case 2: WWW=https://example.com #foo
This is probably fallout from when WWW was moved from pkg-descr to
Makefile.
The anchors still exist on the actual websites too or I removed them.
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.
(Only the first 15 lines of the commit message are shown above )
Fix CONFLICTS entries of multiple ports
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above )
biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc
GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.
