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minimap2: Honour LDFLAGS when linking
biology/minimap2: Update to 2.28 Fix --MD flag Add experimental lr:hqae Changes: https://github.com/lh3/minimap2/releases Reported by: portscout
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
minimap2: Honour CFLAGS/LDFLAGS. Hopefully fixes build on platforms where zlib is installed from pkgsrc.
(biology/minimap2) Updated 2.18 to 2.24 Release 2.24-r1122 (26 December 2021) ------------------------------------- This release improves alignment around long poorly aligned regions. Older minimap2 may chain through such regions in rare cases which may result in missing alignments later. The issue has become worse since the the change of the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This release provides a better solution with a X-drop-like heuristic and by enabling two-bandwidth chaining in the assembly mode. (2.24: 26 December 2021, r1122) Release 2.23-r1111 (18 November 2021) ------------------------------------- Notable changes: * Bugfix: fixed missing alignments around long inversions (#806 and #816). This bug affected v2.19 through v2.22. * Improvement: avoid extremely long mapping time for pathologic reads with highly repeated k-mers not in the reference (#771). Use --q-occ-frac=0 to disable the new heuristic. * Change: use --cap-kalloc=1g by default. (2.23: 18 November 2021, r1111) Release 2.22-r1101 (7 August 2021) ---------------------------------- When choosing the best alignment, this release uses logarithm gap penalty and query-specific mismatch penalty. It improves the sensitivity to long INDELs in repetitive regions. Other notable changes: * Bugfix: fixed an indirect memory leak that may waste a large amount of memory given highly repetitive reference such as a 16S RNA database (#749). All versions of minimap2 have this issue. * New feature: added --cap-kalloc to reduce the peak memory. This option is not enabled by default but may become the default in future releases. Known issue: * Minimap2 may take a long time to map a read (#771). So far it is not clear if this happens to v2.18 and earlier versions. (2.22: 7 August 2021, r1101) Release 2.21-r1071 (6 July 2021) -------------------------------- This release fixed a regression in short-read mapping introduced in v2.19 (#776). It also fixed invalid comparisons of uninitialized variables, though these are harmless (#752). Long-read alignment should be identical to v2.20. (2.21: 6 July 2021, r1071) Release 2.20-r1061 (27 May 2021) -------------------------------- This release fixed a bug in the Python module and improves the command-line compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset, users would get alignments more fragmented than v2.18. This could be an issue for existing pipelines specifying `-r`. This release resolves this issue. (2.20: 27 May 2021, r1061) Release 2.19-r1057 (26 May 2021) -------------------------------- This release includes a few important improvements backported from unimap: * Improvement: more contiguous alignment through long INDELs. This is enabled by the minigraph chaining algorithm. All `asm*` presets now use the new algorithm. They can find INDELs up to 100kb and may be faster for chromosome-long contigs. The default mode and `map*` presets use this algorithm to replace the long-join heuristic. * Improvement: better alignment in highly repetitive regions by rescuing high-occurrence seeds. If the distance between two adjacent seeds is too large, attempt to choose a fraction of high-occurrence seeds in-between. Minimap2 now produces fewer clippings and alignment break points in long satellite regions. * Improvement: allow to specify an interval of k-mer occurrences with `-U`. For repeat-rich genomes, the automatic k-mer occurrence threshold determined by `-f` may be too large and makes alignment impractically slow. The new option protects against such cases. Enabled for `asm*` and `map-hifi`. * New feature: added the `map-hifi` preset for maping PacBio High-Fidelity (HiFi) reads. * Change to the default: apply `--cap-sw-mem=100m` for genomic alignment. * Bugfix: minimap2 could not generate an index file with `-xsr` (#734). This release represents the most signficant algorithmic change since v2.1 in 2017. With features backported from unimap, minimap2 now has similar power to unimap for contig alignment. Unimap will remain an experimental project and is no longer recommended over minimap2. Sorry for reverting the recommendation in short time. (2.19: 26 May 2021, r1057)
biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes
biology: Remove SHA1 hashes for distfiles
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)