Date: Sun, 29 Jul 2018 23:22:51 +0000 From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 230170] biology/htslib: Update 1.9 Message-ID: <bug-230170-7788@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D230170 Bug ID: 230170 Summary: biology/htslib: Update 1.9 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: ports-bugs@FreeBSD.org Reporter: ndowens.fbsd@yandex.com CC: cartwright@asu.edu CC: cartwright@asu.edu Flags: maintainer-feedback?(cartwright@asu.edu) Created attachment 195615 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D195615&action= =3Dedit Update The default SAM version has been changed to 1.6. This is in line with the latest version specification and indicates that HTSlib supports the CG tag = used to store long CIGAR data in BAM format. bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner) Faidx can now index fastq files as well as fasta. The fastq index adds an e= xtra column to the .fai index which gives the offset to the quality values. New interfaces have been added to htslib/faidx.h to read the fastq index and retrieve the quality values. It is possible to open a fastq index as if fas= ta (only sequences will be returned), but not the other way round. (#701) New API interfaces to add or update integer, float and array aux tags. (#69= 4) Add level=3D<number> option to hts_set_opt() to allow the compression level= to be set. Setting level=3D0 enables uncompressed output. (#715) Improved bgzip error reporting. Better error reporting when CRAM reference files can't be opened. (#706) Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences. (#716) Efficiency improvements: Small speed-up for CRAM indexing. Reduce the number of unnecessary wake-ups in the thread pool. (#703) Avoid some memory copies when writing data, notably for uncompressed BG= ZF output. (#703) Bug fixes: Fix multi-region iterator bugs on CRAM files. (#684) Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files. (#687) Fixed synced_bcf_reader() bug when reading contigs multiple times. (#69= 1, reported by @freeseek) Fixed bug where bcf_hdr_set_samples() did not update the sample diction= ary when removing samples. (#692, reported by @freeseek) Fixed bug where the VCF record ref length was calculated incorrectly if= an INFO END tag was present. (71b00a) Fixed warnings found when compiling with gcc 8.1.0. (#700) sam_hdr_read() and sam_hdr_write() will now return an error code if pas= sed a NULL file pointer, instead of crashing. Fixed possible negative array look-up in sam_parse1() that somehow esca= ped previous fuzz testing. (#731, reported by @fCorleone) Fixed bug where cram range queries could incorrectly report an error wh= en using multiple threads. (#734, reported by Brent Pedersen) Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files. (#739, reported by @carsonhh) --=20 You are receiving this mail because: You are the assignee for the bug.=
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