Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database. Typical use cases include:
(1) mapping PacBio or Oxford Nanopore genomic reads to the human genome
(2) finding overlaps between long reads with error rate up to ~15%
(3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
readsagainst a reference genome
(4) aligning Illumina single- or paired-end reads
(5) assembly-to-assembly alignment
(6) full-genome alignment between two closely related species with divergence
below ~15%
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.
biology/minimap2: Update to 2.31
A few bug fixes and enhancements
New subcommands sim2bed and badread2fa
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
all: drop support for FreeBSD 13, mips and risc64sf
Reviewed by: many (*)
Differential Revision: https://reviews.freebsd.org/D55624
Differential Revision: https://reviews.freebsd.org/D55642 (merged in from bofh)
many (*)
acm arrowd brooks cmt dch decke dinoex eduardo fluffy fuz gahr garga
jbeich joerg jrm kai kenrap martymac matthew mfechner michaelo mizhka
nobutaka pkubaj se tagattie thj
Anton Saietskii
GenericRikka
Gert Doering
Jan Bramkamp
Oleh Hushchenkov
Oleksandr Kryvulia
Ralf van der Enden
Yamagi
desktop kde python tcltk office
biology/minimap2: Update to 2.25
New feature to output sequences in secondary alignments
Several minor enhancements and fixes
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
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 )
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.
