CVS commit: pkgsrc/biology/minimap2

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Apr 10 12:36:12 UTC 2024

Modified Files:
        pkgsrc/biology/minimap2: Makefile PLIST distinfo
        pkgsrc/biology/minimap2/patches: patch-Makefile.simde patch-example.c

Log Message:
biology/minimap2: Update to 2.28

Fix --MD flag
Add experimental lr:hqae

Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/minimap2/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/minimap2/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/minimap2/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/minimap2/patches/patch-Makefile.simde \
    pkgsrc/biology/minimap2/patches/patch-example.c

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:1.5 pkgsrc/biology/minimap2/Makefile:1.6
--- pkgsrc/biology/minimap2/Makefile:1.5        Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/Makefile    Wed Apr 10 12:36:12 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.5 2024/03/13 13:54:04 bacon Exp $
+# $NetBSD: Makefile,v 1.6 2024/04/10 12:36:12 bacon Exp $
 
-VERSION=       2.27
+VERSION=       2.28
 DISTNAME=      minimap2-${VERSION}
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}

Index: pkgsrc/biology/minimap2/PLIST
diff -u pkgsrc/biology/minimap2/PLIST:1.3 pkgsrc/biology/minimap2/PLIST:1.4
--- pkgsrc/biology/minimap2/PLIST:1.3   Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/PLIST       Wed Apr 10 12:36:12 2024
@@ -1,3 +1,3 @@
-@comment $NetBSD: PLIST,v 1.3 2024/03/13 13:54:04 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2024/04/10 12:36:12 bacon Exp $
 bin/minimap2
 man/man1/minimap2.1

Index: pkgsrc/biology/minimap2/distinfo
diff -u pkgsrc/biology/minimap2/distinfo:1.6 pkgsrc/biology/minimap2/distinfo:1.7
--- pkgsrc/biology/minimap2/distinfo:1.6        Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/distinfo    Wed Apr 10 12:36:12 2024
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.6 2024/03/13 13:54:04 bacon Exp $
+$NetBSD: distinfo,v 1.7 2024/04/10 12:36:12 bacon Exp $
 
-BLAKE2s (minimap2-2.27.tar.gz) = 92e09196bf9de2c121ce8a3305200760ff9e8ba83d634b106b33297508b5e01d
-SHA512 (minimap2-2.27.tar.gz) = fca5983cbd650b81c6a2caff8ad4d47286467df81ab76646e4fa4b113f0a76d16e4cc8cc5e2f4adaf5c06246ffa099c2728cd0dcba87d808980ed78ee3a029d1
-Size (minimap2-2.27.tar.gz) = 259736 bytes
+BLAKE2s (minimap2-2.28.tar.gz) = 0a0afd89e588dd0d8a93a562264bb5fdfe50f88a18f5f057bf59be51e16bbe0b
+SHA512 (minimap2-2.28.tar.gz) = d8d4bb4381d6effb3eb3e1a66fac7a83bc00c3cf174d2e0537dd4790d0e4a3cc060b92e39ed2e2cafc6e5e713f6fdbee6bac1d279b6b77d4347f77f3e6d3c0d0
+Size (minimap2-2.28.tar.gz) = 260341 bytes
 SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
 SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c

Index: pkgsrc/biology/minimap2/patches/patch-Makefile.simde
diff -u pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.1 pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.2
--- pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.1    Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/patches/patch-Makefile.simde        Wed Apr 10 12:36:12 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile.simde,v 1.1 2024/03/13 13:54:04 bacon Exp $
+$NetBSD: patch-Makefile.simde,v 1.2 2024/04/10 12:36:12 bacon Exp $
 
 # Respect standard env vars
 
Index: pkgsrc/biology/minimap2/patches/patch-example.c
diff -u pkgsrc/biology/minimap2/patches/patch-example.c:1.1 pkgsrc/biology/minimap2/patches/patch-example.c:1.2
--- pkgsrc/biology/minimap2/patches/patch-example.c:1.1 Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/patches/patch-example.c     Wed Apr 10 12:36:12 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-example.c,v 1.1 2024/03/13 13:54:04 bacon Exp $
+$NetBSD: patch-example.c,v 1.2 2024/04/10 12:36:12 bacon Exp $
 
 # Fix data type mismatch