CVS commit: pkgsrc/biology/samtools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Feb 26 23:11:43 UTC 2022

Modified Files:
        pkgsrc/biology/samtools: Makefile PLIST distinfo
        pkgsrc/biology/samtools/patches: patch-Makefile

Log Message:
biology/samtools: Update to 1.15

Several minor enhancements and bug fixes
Changes: https://github.com/samtools/samtools/tags


To generate a diff of this commit:
cvs rdiff -u -r1.13 -r1.14 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/samtools/distinfo
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/samtools/patches/patch-Makefile

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

Modified files:

Index: pkgsrc/biology/samtools/Makefile
diff -u pkgsrc/biology/samtools/Makefile:1.13 pkgsrc/biology/samtools/Makefile:1.14
--- pkgsrc/biology/samtools/Makefile:1.13       Fri Dec 17 15:10:06 2021
+++ pkgsrc/biology/samtools/Makefile    Sat Feb 26 23:11:43 2022
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.13 2021/12/17 15:10:06 bacon Exp $
+# $NetBSD: Makefile,v 1.14 2022/02/26 23:11:43 bacon Exp $
 
-DISTNAME=      samtools-1.14
+DISTNAME=      samtools-1.15
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.4 pkgsrc/biology/samtools/PLIST:1.5
--- pkgsrc/biology/samtools/PLIST:1.4   Fri Dec 17 15:10:06 2021
+++ pkgsrc/biology/samtools/PLIST       Sat Feb 26 23:11:43 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.4 2021/12/17 15:10:06 bacon Exp $
+@comment $NetBSD: PLIST,v 1.5 2022/02/26 23:11:43 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
@@ -28,6 +28,7 @@ man/man1/samtools-bedcov.1
 man/man1/samtools-calmd.1
 man/man1/samtools-cat.1
 man/man1/samtools-collate.1
+man/man1/samtools-consensus.1
 man/man1/samtools-coverage.1
 man/man1/samtools-depad.1
 man/man1/samtools-depth.1
@@ -39,6 +40,7 @@ man/man1/samtools-fixmate.1
 man/man1/samtools-flags.1
 man/man1/samtools-flagstat.1
 man/man1/samtools-fqidx.1
+man/man1/samtools-head.1
 man/man1/samtools-idxstats.1
 man/man1/samtools-import.1
 man/man1/samtools-index.1

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.7 pkgsrc/biology/samtools/distinfo:1.8
--- pkgsrc/biology/samtools/distinfo:1.7        Fri Dec 17 15:10:06 2021
+++ pkgsrc/biology/samtools/distinfo    Sat Feb 26 23:11:43 2022
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.7 2021/12/17 15:10:06 bacon Exp $
+$NetBSD: distinfo,v 1.8 2022/02/26 23:11:43 bacon Exp $
 
-BLAKE2s (samtools-1.14.tar.gz) = 86b0e03b47d62619507b3b3284ac82689caa962da424c4af03f6690113a2ea50
-SHA512 (samtools-1.14.tar.gz) = fafc256fff8d2725b8a8ff4555cdb14aa0d32eec3a9afc6ff8ab7b474deed48f2a108805cc8f020cc3a28eec0d04034784d1af340bf89eb3c5f6ef3f262ac489
-Size (samtools-1.14.tar.gz) = 4933354 bytes
+BLAKE2s (samtools-1.15.tar.gz) = b37f18ce7134f921f1e8b5ebb087ad88b387934080742f26708bbecf9ddb5df7
+SHA512 (samtools-1.15.tar.gz) = fad213b6d7eb8885b67642ad7235fb35a923238c13fac7fde501f0d8093fa90d49539e895691bc61a94f6d25e8cdfc4e2c4e94ff0ea91ceee248d5140f561cd6
+Size (samtools-1.15.tar.gz) = 4970205 bytes
 SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d

Index: pkgsrc/biology/samtools/patches/patch-Makefile
diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.3 pkgsrc/biology/samtools/patches/patch-Makefile:1.4
--- pkgsrc/biology/samtools/patches/patch-Makefile:1.3  Fri Dec 17 15:10:06 2021
+++ pkgsrc/biology/samtools/patches/patch-Makefile      Sat Feb 26 23:11:43 2022
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.3 2021/12/17 15:10:06 bacon Exp $
+$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:11:43 bacon Exp $
 
 # Respect pkgsrc env