CVS commit: pkgsrc/biology/htslib

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Jul  5 11:00:16 UTC 2022

Modified Files:
        pkgsrc/biology/htslib: Makefile distinfo

Log Message:
htslib: updated to 1.15.1

1.15.1

Security fix: Fixed broken error reporting in the sam_cap_mapq() function, due to a missing hts_log() parameter. Prior to this fix it was possible to abuse the log message format string by passing a 
specially crafted alignment record to this function.

HTSlib now uses libhtscodecs release 1.2.2. This fixes a number of bugs where invalid compressed data could trigger usage of uninitialised values.

Fixed excessive memory used by multi-threaded SAM output on long reads.

Fixed a bug where tabix would misinterpret region specifiers starting at position 0. It will also now warn if the file being indexed is supposed to be 1-based but has positions less than or equal to 
0.

The VCF header parser will now issue a warning if it finds an INFO header with Type=Flag but Number not equal to 0. It will also ignore the incorrect Number so the flag can be used.


To generate a diff of this commit:
cvs rdiff -u -r1.26 -r1.27 pkgsrc/biology/htslib/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/htslib/distinfo

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

Modified files:

Index: pkgsrc/biology/htslib/Makefile
diff -u pkgsrc/biology/htslib/Makefile:1.26 pkgsrc/biology/htslib/Makefile:1.27
--- pkgsrc/biology/htslib/Makefile:1.26 Tue Jun 28 11:31:00 2022
+++ pkgsrc/biology/htslib/Makefile      Tue Jul  5 11:00:16 2022
@@ -1,10 +1,9 @@
-# $NetBSD: Makefile,v 1.26 2022/06/28 11:31:00 wiz Exp $
+# $NetBSD: Makefile,v 1.27 2022/07/05 11:00:16 adam Exp $
 
-DISTNAME=      htslib-1.15
-PKGREVISION=   1
+DISTNAME=      htslib-1.15.1
 CATEGORIES=    biology
 # Github-generated distfiles are incomplete, use custom tarballs instead
-MASTER_SITES=  https://github.com/samtools/htslib/releases/download/${PKGVERSION_NOREV}/
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/htslib/releases/download/${PKGVERSION_NOREV}/}
 EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    bacon%NetBSD.org@localhost

Index: pkgsrc/biology/htslib/distinfo
diff -u pkgsrc/biology/htslib/distinfo:1.8 pkgsrc/biology/htslib/distinfo:1.9
--- pkgsrc/biology/htslib/distinfo:1.8  Sat Feb 26 23:08:43 2022
+++ pkgsrc/biology/htslib/distinfo      Tue Jul  5 11:00:16 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.8 2022/02/26 23:08:43 bacon Exp $
+$NetBSD: distinfo,v 1.9 2022/07/05 11:00:16 adam Exp $
 
-BLAKE2s (htslib-1.15.tar.bz2) = 74f4c5e815b6276507762ca956232a44784bd6d085534c2853cbaf22a29127ce
-SHA512 (htslib-1.15.tar.bz2) = b87ce3eaa63a731d812953129f1c9aa857fe896ea9e924b7eb92173d8e624dd45e5582b3a97e7120ff7fe339e4d40148077424029626f50372b3f164093aa6cc
-Size (htslib-1.15.tar.bz2) = 4141168 bytes
+BLAKE2s (htslib-1.15.1.tar.bz2) = 7d7498964c0bd934ba24450ebb86584f82606df788f3f126d76fd9e8fdd9d9b6
+SHA512 (htslib-1.15.1.tar.bz2) = 69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
+Size (htslib-1.15.1.tar.bz2) = 4141140 bytes