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authoradam <adam@pkgsrc.org>2022-07-05 11:00:16 +0000
committeradam <adam@pkgsrc.org>2022-07-05 11:00:16 +0000
commitd7c5dbfb2b29051473ca984120cf89bdc5749b3a (patch)
tree54ad19098da17e0097b3d4ccea20a0635812feff /security/libb2/patches
parentd788bd0ab040e7f105f6a8acd5179edcee517252 (diff)
downloadpkgsrc-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.
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