Bump mappy from 2.17 to 2.28

[dependabot[bot]]

Bumps mappy from 2.17 to 2.28.

Release notes

Sourced from mappy's releases.

Minimap2-2.28 (r1209)

Notable changes to minimap2:

• Bugfix: --MD was not working properly due to the addition of --ds in the last release (#1181 and #1182).

• New feature: added an experimental preset lr:hqae for aligning accurate long reads back to their assembly. It has been observed that map-hifi and lr:hq may produce many wrong alignments around centromeres when accurate long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid assembly constructed from them. This new preset produces much more accurate alignment. It is still experimental and may be subjective to changes in future.

• Change: reduced the default --cap-kalloc to 500m to lower the peak memory consumption (#855).

Notable changes to mappy:

• Bugfix: mappy option struct was out of sync with minimap2 (#1177).

Minimap2 should output identical alignments to v2.27.

(2.28: 27 March 2024, r1209)

Minimap2-2.27 (r1193)

Notable changes to minimap2:

• New feature: added the lr:hq preset for accurate long reads at ~1% error rate. This was suggested by Oxford Nanopore developers (#1127). Whether this preset works well for PacBio HiFi reads has not been tested.

• New feature: added the map-iclr preset for Illumina Complete Long Reads (#1069), provided by Illumina developers.

• New feature: added option -b to specify mismatch penalty for base transitions (i.e. A-to-G or C-to-T changes).

• New feature: added option --ds to generate a new ds:Z tag that indicates uncertainty in INDEL positions. It is an extension to cs. The mgutils-es6.js script in minigraph parses ds.

• Bugfix: avoided a NULL pointer dereference (#1154). This would not have an effect on most systems but would still be good to fix.

• Bugfix: reverted the value of ms:i to pre-2.22 versions (#1146). This was an oversight. See fcd4df2 for details.

Notable changes to paftools.js and mappy:

... (truncated)

Changelog

Sourced from mappy's changelog.

Release 2.28-r1209 (27 March 2024)

Notable changes to minimap2:

• Bugfix: --MD was not working properly due to the addition of --ds in the last release (#1181 and #1182).

• New feature: added an experimental preset lq:hqae for aligning accurate long reads back to their assembly. It has been observed that map-hifi and lr:hq may produce many wrong alignments around centromeres when accurate long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid assembly constructed from them. This new preset produces much more accurate alignment. It is still experimental and may be subjective to changes in future.

• Change: reduced the default --cap-kalloc to 500m to lower the peak memory consumption (#855).

Notable changes to mappy:

• Bugfix: mappy option struct was out of sync with minimap2 (#1177).

Minimap2 should output identical alignments to v2.27.

(2.28: 27 March 2024, r1209)

Release 2.27-r1193 (12 March 2024)

Notable changes to minimap2:

• New feature: added the lr:hq preset for accurate long reads at ~1% error rate. This was suggested by Oxford Nanopore developers (#1127). It is not clear if this preset also works well for PacBio HiFi reads.

• New feature: added the map-iclr preset for Illumina Complete Long Reads (#1069), provided by Illumina developers.

• New feature: added option -b to specify mismatch penalty for base transitions (i.e. A-to-G or C-to-T changes).

• New feature: added option --ds to generate a new ds:Z tag that indicates uncertainty in INDEL positions. It is an extension to cs. The mgutils-es6.js script in minigraph parses ds.

• Bugfix: avoided a NULL pointer dereference (#1154). This would not have an effect on most systems but would still be good to fix.

... (truncated)

Commits

• 8170693 Release minimap2-2.28 (r1209)
• e3d8c70 r1208: reverted RMQ gap coefficient
• 119bdc6 r1207: reduced cap_kalloc from 1G to 500M
• 89d4d21 r1206: enabled RMQ for lr:hqae
• f51ff1a r1205: updated lr:hqae
• 27b254e backup; DON'T USE!!!
• c881b14 r1203: added preset lr:hqae
• f18dadb r1202: halved RMQ gap cost
• a83b8fe r1201: renamed --dbg-seed-freq to --dbg-seed-occ
• c22bfe7 r1200: added --rmq-inner and --dbg-seed-freq
• Additional commits viewable in compare view

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[Donaim]

@dependabot recreate

[Donaim]

@dependabot recreate

[dependabot[bot]]

Looks like mappy is up-to-date now, so this is no longer needed.