Subject: CVS commit: pkgsrc/biology/htslib
From: Adam Ciarcinski
Date: 2022-07-05 13:00:16
Message id: 20220705110016.31C2FFB1A@cvs.NetBSD.org

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.

Files:
RevisionActionfile
1.27modifypkgsrc/biology/htslib/Makefile
1.9modifypkgsrc/biology/htslib/distinfo