[pkgsrc/trunk]: pkgsrc/biology/htslib htslib: updated to 1.15.1

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/4b9f647f2911
branches:  trunk
changeset: 381366:4b9f647f2911
user:      adam <adam%pkgsrc.org@localhost>
date:      Tue Jul 05 11:00:16 2022 +0000

description:
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.

diffstat:

 biology/htslib/Makefile |  7 +++----
 biology/htslib/distinfo |  8 ++++----
 2 files changed, 7 insertions(+), 8 deletions(-)

diffs (30 lines):

diff -r cc5d852e7e11 -r 4b9f647f2911 biology/htslib/Makefile
--- a/biology/htslib/Makefile   Tue Jul 05 10:45:52 2022 +0000
+++ b/biology/htslib/Makefile   Tue Jul 05 11:00:16 2022 +0000
@@ -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
diff -r cc5d852e7e11 -r 4b9f647f2911 biology/htslib/distinfo
--- a/biology/htslib/distinfo   Tue Jul 05 10:45:52 2022 +0000
+++ b/biology/htslib/distinfo   Tue Jul 05 11:00:16 2022 +0000
@@ -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