[pkgsrc/trunk]: pkgsrc/biology/samtools biology/samtools: Update to 1.14

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/7479a4dcc11f
branches:  trunk
changeset: 771347:7479a4dcc11f
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Fri Dec 17 15:10:06 2021 +0000

description:
biology/samtools: Update to 1.14

Numerous fixes and enhancements since 1.12

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

diffstat:

 biology/samtools/Makefile               |  6 ++----
 biology/samtools/PLIST                  |  4 +++-
 biology/samtools/distinfo               |  8 ++++----
 biology/samtools/patches/patch-Makefile |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diffs (69 lines):

diff -r fd4d77f04d78 -r 7479a4dcc11f biology/samtools/Makefile
--- a/biology/samtools/Makefile Fri Dec 17 15:01:37 2021 +0000
+++ b/biology/samtools/Makefile Fri Dec 17 15:10:06 2021 +0000
@@ -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 @@
 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"
diff -r fd4d77f04d78 -r 7479a4dcc11f biology/samtools/PLIST
--- a/biology/samtools/PLIST    Fri Dec 17 15:01:37 2021 +0000
+++ b/biology/samtools/PLIST    Fri Dec 17 15:10:06 2021 +0000
@@ -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-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-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
diff -r fd4d77f04d78 -r 7479a4dcc11f biology/samtools/distinfo
--- a/biology/samtools/distinfo Fri Dec 17 15:01:37 2021 +0000
+++ b/biology/samtools/distinfo Fri Dec 17 15:10:06 2021 +0000
@@ -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
diff -r fd4d77f04d78 -r 7479a4dcc11f biology/samtools/patches/patch-Makefile
--- a/biology/samtools/patches/patch-Makefile   Fri Dec 17 15:01:37 2021 +0000
+++ b/biology/samtools/patches/patch-Makefile   Fri Dec 17 15:10:06 2021 +0000
@@ -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