CVS commit: pkgsrc/biology/samtools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Feb 25 13:52:39 UTC 2023

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

Log Message:
biology/samtools: Update to 1.17

Numerous enhancements and bug fixes

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


To generate a diff of this commit:
cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/samtools/distinfo
cvs rdiff -u -r1.4 -r1.5 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:1.18 pkgsrc/biology/samtools/Makefile:1.19
--- pkgsrc/biology/samtools/Makefile:1.18       Wed Dec 28 15:27:17 2022
+++ pkgsrc/biology/samtools/Makefile    Sat Feb 25 13:52:39 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.18 2022/12/28 15:27:17 bacon Exp $
+# $NetBSD: Makefile,v 1.19 2023/02/25 13:52:39 bacon Exp $
 
-DISTNAME=      samtools-1.16.1
+DISTNAME=      samtools-1.17
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 GITHUB_RELEASE=        ${PKGVERSION_NOREV}

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.6 pkgsrc/biology/samtools/PLIST:1.7
--- pkgsrc/biology/samtools/PLIST:1.6   Tue Dec 13 10:28:01 2022
+++ pkgsrc/biology/samtools/PLIST       Sat Feb 25 13:52:39 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.6 2022/12/13 10:28:01 adam Exp $
+@comment $NetBSD: PLIST,v 1.7 2023/02/25 13:52:39 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
@@ -30,6 +30,7 @@ man/man1/samtools-cat.1
 man/man1/samtools-collate.1
 man/man1/samtools-consensus.1
 man/man1/samtools-coverage.1
+man/man1/samtools-cram-size.1
 man/man1/samtools-depad.1
 man/man1/samtools-depth.1
 man/man1/samtools-dict.1
@@ -51,6 +52,7 @@ man/man1/samtools-phase.1
 man/man1/samtools-quickcheck.1
 man/man1/samtools-reference.1
 man/man1/samtools-reheader.1
+man/man1/samtools-reset.1
 man/man1/samtools-rmdup.1
 man/man1/samtools-samples.1
 man/man1/samtools-sort.1

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.9 pkgsrc/biology/samtools/distinfo:1.10
--- pkgsrc/biology/samtools/distinfo:1.9        Tue Dec 13 10:28:01 2022
+++ pkgsrc/biology/samtools/distinfo    Sat Feb 25 13:52:39 2023
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.9 2022/12/13 10:28:01 adam Exp $
+$NetBSD: distinfo,v 1.10 2023/02/25 13:52:39 bacon Exp $
 
-BLAKE2s (samtools-1.16.1.tar.bz2) = 45ca326da1c2aa560fde2d582b58150b71f05d72ff996c9ae97427ef22b018a0
-SHA512 (samtools-1.16.1.tar.bz2) = f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
-Size (samtools-1.16.1.tar.bz2) = 8217689 bytes
+BLAKE2s (samtools-1.17.tar.bz2) = 9ab61bddae955190736abf7e9198ee869396a74e195166df38ebb652fe4bc7c7
+SHA512 (samtools-1.17.tar.bz2) = 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
+Size (samtools-1.17.tar.bz2) = 8605080 bytes
 SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d

Index: pkgsrc/biology/samtools/patches/patch-Makefile
diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.4 pkgsrc/biology/samtools/patches/patch-Makefile:1.5
--- pkgsrc/biology/samtools/patches/patch-Makefile:1.4  Sat Feb 26 23:11:43 2022
+++ pkgsrc/biology/samtools/patches/patch-Makefile      Sat Feb 25 13:52:39 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:11:43 bacon Exp $
+$NetBSD: patch-Makefile,v 1.5 2023/02/25 13:52:39 bacon Exp $
 
 # Respect pkgsrc env