---
- branch: MAIN
  date: Sun Mar 13 08:05:07 UTC 2022
  files:
  - new: '1.3'
    old: '1.2'
    path: pkgsrc/biology/minimap2/Makefile
    pathrev: pkgsrc/biology/minimap2/Makefile@1.3
    type: modified
  - new: '1.4'
    old: '1.3'
    path: pkgsrc/biology/minimap2/distinfo
    pathrev: pkgsrc/biology/minimap2/distinfo@1.4
    type: modified
  id: 20220313T080507Z.1e556bf54334bbc88927f67d763fad7af455cc9d
  log: |
    (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)
  module: pkgsrc
  subject: 'CVS commit: pkgsrc/biology/minimap2'
  unixtime: '1647158707'
  user: mef