Minimap2-2.19 (r1057)

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 mapping 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 significant 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.

(2.20: 26 May 2021, r1055)