Minimap2-2.29 (r1283)

Notable changes to minimap2:

• New feature: added the splice:sr preset for short RNA-seq read alignment.
  Users may use -j to specify known gene annotation to improve spliced
  alignment close to the ends of short reads. Also added --write-junc and
  --pass1 for 2-pass short-read RNA-seq alignment.

• Experimental feature: read splice scores from a file specified by --spsc
  and consider the scores during base alignment. The feature makes it possible
  to apply advanced splice models and to improve spliced alignment.

• Change: adjusted the mapping quality calculation for spliced alignment.

• Bugfixes: a) missing overlap alignment when base alignment is requested
  (#969); b) incorrect summary information for long genomes (#1192); c)
  missing parameter check for --score-N (#1226).

• Improvement: a) warn about absent junction files (#1229); b) report an error
  if a wrong preset prefixed with "splice" is specified (#589).

Notable changes to mappy:

• Improvement: allow passing read name (#1260)

• Improvement: exposed score for ambiguous bases (#1240)

Minimap2 now supports short/long genomic/RNA-seq read alignment along with
contig alignment and all-vs-all read overlapping. It produces identical genomic
long-read or contig alignment to v2.27. Short genomic read alignment and the
mapping quality of long RNA-seq read alignment may slightly differ in very rare
cases.

(2.29: 18 April 2025, r1283)