CVS commit: pkgsrc/biology/minimap2

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Mar 13 08:05:07 UTC 2022

Modified Files:
        pkgsrc/biology/minimap2: Makefile distinfo

Log Message:
(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)


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/minimap2/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/minimap2/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/minimap2/Makefile
diff -u pkgsrc/biology/minimap2/Makefile:1.2 pkgsrc/biology/minimap2/Makefile:1.3
--- pkgsrc/biology/minimap2/Makefile:1.2        Sat May 29 17:35:18 2021
+++ pkgsrc/biology/minimap2/Makefile    Sun Mar 13 08:05:07 2022
@@ -1,20 +1,16 @@
-# $NetBSD: Makefile,v 1.2 2021/05/29 17:35:18 brook Exp $
+# $NetBSD: Makefile,v 1.3 2022/03/13 08:05:07 mef Exp $
 
-GITHUB_PROJECT=        minimap2
-GITHUB_TAG=    refs/tags/v2.18
-DISTNAME=      v2.18
-PKGNAME=       ${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
-PKGREVISION=   1
+VERSION=       2.24
+DISTNAME=      minimap2-${VERSION}
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
-DIST_SUBDIR=   ${GITHUB_PROJECT}
+GITHUB_TAG=    v${VERSION}
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 HOMEPAGE=      https://github.com/lh3/minimap2
 COMMENT=       Sequence alignment program for noisy, long reads
 LICENSE=       mit
 
-WRKSRC=                ${WRKDIR}/minimap2-2.18
 USE_TOOLS+=    gmake
 
 INSTALLATION_DIRS+=    bin ${PKGMANDIR}/man1

Index: pkgsrc/biology/minimap2/distinfo
diff -u pkgsrc/biology/minimap2/distinfo:1.3 pkgsrc/biology/minimap2/distinfo:1.4
--- pkgsrc/biology/minimap2/distinfo:1.3        Tue Oct 26 10:03:41 2021
+++ pkgsrc/biology/minimap2/distinfo    Sun Mar 13 08:05:07 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:41 nia Exp $
+$NetBSD: distinfo,v 1.4 2022/03/13 08:05:07 mef Exp $
 
-BLAKE2s (minimap2/v2.18.tar.gz) = 89363e4623696788351880a672a1150e27912d7be694b131a7edc88b116ac265
-SHA512 (minimap2/v2.18.tar.gz) = b2521ec453b836330eb6dcf87969e6171e7c1d53cee2767e6a36a0c422a9fa14c83a085b75371343ae119d719829bfe26b5d9f0008ccad1ac0f51b391a984860
-Size (minimap2/v2.18.tar.gz) = 231187 bytes
+BLAKE2s (minimap2-2.24.tar.gz) = fad5bbbfd6563f32ffe046528758eca23b071386847b1a93d3388f5be205de5b
+SHA512 (minimap2-2.24.tar.gz) = f53a28ce5cd8624fbc5e964dc58edfa27ecea5f253cd49cb7b57396a40810b673392ebf323f0fb5d3b6ef82d4a9a96b025581aee10246e3c8d59e954819876e7
+Size (minimap2-2.24.tar.gz) = 253050 bytes