CVS commit: pkgsrc/biology/samtools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Dec 17 15:10:06 UTC 2021

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

Log Message:
biology/samtools: Update to 1.14

Numerous fixes and enhancements since 1.12

Changes: https://github.com/samtools/samtools/tags


To generate a diff of this commit:
cvs rdiff -u -r1.12 -r1.13 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/samtools/distinfo
cvs rdiff -u -r1.2 -r1.3 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:1.12 pkgsrc/biology/samtools/Makefile:1.13
--- pkgsrc/biology/samtools/Makefile:1.12       Mon May 24 19:49:11 2021
+++ pkgsrc/biology/samtools/Makefile    Fri Dec 17 15:10:06 2021
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.12 2021/05/24 19:49:11 wiz Exp $
+# $NetBSD: Makefile,v 1.13 2021/12/17 15:10:06 bacon Exp $
 
-DISTNAME=      samtools-1.12
-PKGREVISION=   1
+DISTNAME=      samtools-1.14
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 
@@ -35,7 +34,6 @@ TEST_TARGET=          test
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
 
-BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
 .include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../lang/python/application.mk"

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.3 pkgsrc/biology/samtools/PLIST:1.4
--- pkgsrc/biology/samtools/PLIST:1.3   Sat Mar 20 18:17:07 2021
+++ pkgsrc/biology/samtools/PLIST       Fri Dec 17 15:10:06 2021
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2021/12/17 15:10:06 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
@@ -40,6 +40,7 @@ man/man1/samtools-flags.1
 man/man1/samtools-flagstat.1
 man/man1/samtools-fqidx.1
 man/man1/samtools-idxstats.1
+man/man1/samtools-import.1
 man/man1/samtools-index.1
 man/man1/samtools-markdup.1
 man/man1/samtools-merge.1
@@ -48,6 +49,7 @@ man/man1/samtools-phase.1
 man/man1/samtools-quickcheck.1
 man/man1/samtools-reheader.1
 man/man1/samtools-rmdup.1
+man/man1/samtools-samples.1
 man/man1/samtools-sort.1
 man/man1/samtools-split.1
 man/man1/samtools-stats.1

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.6 pkgsrc/biology/samtools/distinfo:1.7
--- pkgsrc/biology/samtools/distinfo:1.6        Tue Oct 26 10:03:44 2021
+++ pkgsrc/biology/samtools/distinfo    Fri Dec 17 15:10:06 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.6 2021/10/26 10:03:44 nia Exp $
+$NetBSD: distinfo,v 1.7 2021/12/17 15:10:06 bacon Exp $
 
-BLAKE2s (samtools-1.12.tar.gz) = 5da0299084134f46286b6cae23738ff493b1144a660fea417f05d36bd78cc382
-SHA512 (samtools-1.12.tar.gz) = 7f468a4740610c2fdc42d8f020d3082e5b2b2e73b0c2dfc19b212ca259d703f34f7df0922e409a94500ccc0357d4d46306035be29c23a523ef6e959022f9d1db
-Size (samtools-1.12.tar.gz) = 4528460 bytes
+BLAKE2s (samtools-1.14.tar.gz) = 86b0e03b47d62619507b3b3284ac82689caa962da424c4af03f6690113a2ea50
+SHA512 (samtools-1.14.tar.gz) = fafc256fff8d2725b8a8ff4555cdb14aa0d32eec3a9afc6ff8ab7b474deed48f2a108805cc8f020cc3a28eec0d04034784d1af340bf89eb3c5f6ef3f262ac489
+Size (samtools-1.14.tar.gz) = 4933354 bytes
 SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d

Index: pkgsrc/biology/samtools/patches/patch-Makefile
diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.2 pkgsrc/biology/samtools/patches/patch-Makefile:1.3
--- pkgsrc/biology/samtools/patches/patch-Makefile:1.2  Sat Mar 20 18:17:07 2021
+++ pkgsrc/biology/samtools/patches/patch-Makefile      Fri Dec 17 15:10:06 2021
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
+$NetBSD: patch-Makefile,v 1.3 2021/12/17 15:10:06 bacon Exp $
 
 # Respect pkgsrc env