Tags: dozy/htslib
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htslib release 1.9: * If `./configure` fails, `make` will stop working until either configure is re-run successfully, or `make distclean` is used. This makes configuration failures more obvious. (samtools#711, thanks to John Marshall) * 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' (samtools#682, thanks to @sd4B75bJ, @jrayner) * Faidx can now index fastq files as well as fasta. The fastq index adds an extra 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 fasta (only sequences will be returned), but not the other way round. (samtools#701) * New API interfaces to add or update integer, float and array aux tags. (samtools#694) * Add `level=<number>` option to `hts_set_opt()` to allow the compression level to be set. Setting `level=0` enables uncompressed output. (samtools#715) * Improved bgzip error reporting. * Better error reporting when CRAM reference files can't be opened. (samtools#706) * Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences. (samtools#716) * Efficiency improvements: - Small speed-up for CRAM indexing. - Reduce the number of unnecessary wake-ups in the thread pool. (samtools#703) - Avoid some memory copies when writing data, notably for uncompressed BGZF output. (samtools#703) * Bug fixes: - Fix multi-region iterator bugs on CRAM files. (samtools#684) - Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files. (samtools#687) - Fixed synced_bcf_reader() bug when reading contigs multiple times. (samtools#691, reported by @freeseek) - Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when removing samples. (samtools#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. (samtools#700) - sam_hdr_read() and sam_hdr_write() will now return an error code if passed a NULL file pointer, instead of crashing. - Fixed possible negative array look-up in sam_parse1() that somehow escaped previous fuzz testing. (samtools#731, reported by @fCorleone) - Fixed bug where cram range queries could incorrectly report an error when using multiple threads. (samtools#734, reported by Brent Pedersen) - Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files. (samtools#739, reported by @carsonhh)
htslib release 1.8: * The URL to get sequences from the EBI reference server has been changed to https://. This is because the EBI no longer serve sequences via plain HTTP - requests to the http:// endpoint just get redirected. HTSlib needs to be linked against libcurl to download https:// URLs, so CRAM users who want to get references from the EBI will need to run configure and ensure libcurl support is enabled using the --enable-libcurl option. * Added libdeflate as a build option for alternative faster compression and decompression. Results vary by CPU but compression should be twice as fast and decompression faster. * It is now possible to set the compression level in bgzip. (samtools#675; thanks to Nathan Weeks). * bgzip now gets its own manual page. * CRAM encoding now stored MD and NM tags verbatim where the reference contains 'N' characters, to work around ambiguities in the SAM specification (samtools samtools#717/762). Also added "store_md" and "store_nm" cram-options for forcing these tags to be stored at all locations. This is best when combined with a subsequent decode_md=0 option while reading CRAM. * Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of references with `-T ref.fa`. (samtools#654; reported by Chris Saunders) * CRAM multi-threading bugs fixed: don't try to call flush on reading; processing of multiple range queries; problems with multi-slice containers. * Fixed crashes caused when decoding some cramtools produced CRAM files. * Fixed a couple of minor rANS issues with handling invalid data. * Fixed bug where probaln_glocal() tried to allocate far more memory than needed when the query sequence was much longer than the reference. This caused crashes in samtools and bcftools mpileup when used on data with very long reads. (samtools#572, problem reported by Felix Bemm via minimap2). * sam_prop_realn() now returns -1 (the same value as for unmapped reads) on reads that do not include at least one 'M', 'X' or '=' CIGAR operator, and no longer adds BQ or ZQ tags. BAQ adjustments are only made to bases covered by these operators so there is no point in trying to align reads that do not have them. (samtools#572)
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