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| author | adam <adam@pkgsrc.org> | 2022-07-05 11:00:16 +0000 |
|---|---|---|
| committer | adam <adam@pkgsrc.org> | 2022-07-05 11:00:16 +0000 |
| commit | d7c5dbfb2b29051473ca984120cf89bdc5749b3a (patch) | |
| tree | 54ad19098da17e0097b3d4ccea20a0635812feff /biology | |
| parent | d788bd0ab040e7f105f6a8acd5179edcee517252 (diff) | |
| download | pkgsrc-d7c5dbfb2b29051473ca984120cf89bdc5749b3a.tar.gz | |
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 (limited to 'biology')
| -rw-r--r-- | biology/htslib/Makefile | 7 | ||||
| -rw-r--r-- | biology/htslib/distinfo | 8 |
2 files changed, 7 insertions, 8 deletions
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index 4e65e89c242..4a9149f9a51 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -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 diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo index 4c59d33b696..9c3e1669053 100644 --- a/biology/htslib/distinfo +++ b/biology/htslib/distinfo @@ -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 |