head 1.3; access; symbols pkgsrc-2023Q4:1.2.0.22 pkgsrc-2023Q4-base:1.2 pkgsrc-2023Q3:1.2.0.20 pkgsrc-2023Q3-base:1.2 pkgsrc-2023Q2:1.2.0.18 pkgsrc-2023Q2-base:1.2 pkgsrc-2023Q1:1.2.0.16 pkgsrc-2023Q1-base:1.2 pkgsrc-2022Q4:1.2.0.14 pkgsrc-2022Q4-base:1.2 pkgsrc-2022Q3:1.2.0.12 pkgsrc-2022Q3-base:1.2 pkgsrc-2022Q2:1.2.0.10 pkgsrc-2022Q2-base:1.2 pkgsrc-2022Q1:1.2.0.8 pkgsrc-2022Q1-base:1.2 pkgsrc-2021Q4:1.2.0.6 pkgsrc-2021Q4-base:1.2 pkgsrc-2021Q3:1.2.0.4 pkgsrc-2021Q3-base:1.2 pkgsrc-2021Q2:1.2.0.2 pkgsrc-2021Q2-base:1.2; locks; strict; comment @# @; 1.3 date 2024.03.13.13.54.04; author bacon; state Exp; branches; next 1.2; commitid n9gocd8So9chk02F; 1.2 date 2021.05.29.17.35.18; author brook; state Exp; branches; next 1.1; commitid wHUgJRLW44vlj4VC; 1.1 date 2021.05.26.18.49.20; author brook; state Exp; branches; next ; commitid Nz29gmMUs97JOGUC; desc @@ 1.3 log @biology/minimap2: Update to 2.27 Several new features and bug fixes since 2.24 Changes: https://github.com/lh3/minimap2/releases Reported by: portscout @ text @@@comment $NetBSD$ bin/minimap2 man/man1/minimap2.1 @ 1.2 log @biology/minimap2: install minimap2 program instead of python binding The distfile for minimap2 includes two different components: (i) the minimap2 sequence mapping program itself, and (ii) a python binding generally referred to as mappy. The initial version of this package included only the python binding. However, it is more appropriate that the minimap2 package should contain the program of the same name, and a new package be created with the name mappy for the python binding. Splitting these into two packages makes sense, because this allows users to install the minimap2 package without python dependencies. @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.1 2021/05/26 18:49:20 brook Exp $ @ 1.1 log @biology/minimap2: add minimap 2.18 ## Users' Guide 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 reads against 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%. For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint. Release 2.18-r1015 (9 April 2021) --------------------------------- This release fixes multiple rare bugs in minimap2 and adds additional functionality to paftools.js. Changes to minimap2: * Bugfix: a rare segfault caused by an off-by-one error (#489) * Bugfix: minimap2 segfaulted due to an uninitilized variable (#622 and #625). * Bugfix: minimap2 parsed spaces as field separators in BED (#721). This led to issues when the BED name column contains spaces. * Bugfix: minimap2 `--split-prefix` did not work with long reference names (#394). * Bugfix: option `--junc-bonus` didn't work (#513) * Bugfix: minimap2 didn't return 1 on I/O errors (#532) * Bugfix: the `de:f` tag (sequence divergence) could be negative if there were ambiguous bases * Bugfix: fixed two undefined behaviors caused by calling memcpy() on zero-length blocks (#443) * Bugfix: there were duplicated SAM @@SQ lines if option `--split-prefix` is in use (#400 and #527) * Bugfix: option -K had to be smaller than 2 billion (#491). This was caused by a 32-bit integer overflow. * Improvement: optionally compile against SIMDe (#597). Minimap2 should work with IBM POWER CPUs, though this has not been tested. To compile with SIMDe, please use `make -f Makefile.simde`. * Improvement: more informative error message for I/O errors (#454) and for FASTQ parsing errors (#510) * Improvement: abort given malformatted RG line (#541) * Improvement: better formula to estimate the `dv:f` tag (approximate sequence divergence). See DOI:10.1101/2021.01.15.426881. * New feature: added the `--mask-len` option to fine control the removal of redundant hits (#659). The default behavior is unchanged. Changes to mappy: * Bugfix: mappy caused segmentation fault if the reference index is not present (#413). * Bugfix: fixed a memory leak via 238b6bb3 * Change: always require Cython to compile the mappy module (#723). Older mappy packages at PyPI bundled the C source code generated by Cython such that end users did not need to install Cython to compile mappy. However, as Python 3.9 is breaking backward compatibility, older mappy does not work with Python 3.9 anymore. We have to add this Cython dependency as a workaround. Changes to paftools.js: * Bugfix: the "part10-" line from asmgene was wrong (#581) * Improvement: compatibility with GTF files from GenBank (#422) * New feature: asmgene also checks missing multi-copy genes * New feature: added the misjoin command to evaluate large-scale misjoins and megabase-long inversions. Although given the many bug fixes and minor improvements, the core algorithm stays the same. This version of minimap2 produces nearly identical alignments to v2.17 except very rare corner cases. Now unimap is recommended over minimap2 for aligning long contigs against a reference genome. It often takes less wall-clock time and is much more sensitive to long insertions and deletions. (2.18: 9 April 2021, r1015) @ text @d1 3 a3 9 @@comment $NetBSD$ bin/minimap2.py ${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/PKG-INFO ${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/SOURCES.txt ${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/dependency_links.txt ${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/top_level.txt ${PYSITELIB}/mappy.so share/examples/minimap2/README.md share/examples/minimap2/cookbook.md @