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NEW. Add ref-cache, a caching proxy for reference sequences. This is a local server of reference sequences, for use when encoding or decoding CRAM files that use reference-based compression. (PR #1911, PR #1921, PR #1922)
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Add support for matching VCF lines by ID. (PR #1844, addresses issue samtools/bcftools#1739 reported by Han Cao)
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Make it possible to test for VCF_REF as declared in the documentation. (PR #1879)
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Updated VCF code to work with VCF 4.4 prefixed phasing info. (PR #1861, fixes #1847. Reported by John Marshall)
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Use the highest VCF version when merging headers. (PR #1912, see samtools/bcftools#2395 and samtools/bcftools#2404)
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Update RLEN calculation for VCF 4.4 and 4.5. (PR #1897, fixes #1820. Reported by Dave Lawrence)
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Convert U to T instead of U to N when sam_parsing. Though SAM format itself can contain U the BAM format cannot. (PR #1854, fixes samtools/samtools#2131 reported by James Ferguson)
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Add an hts_crc32 function to use zlib or libdeflate. The libdeflate crc32 function is faster than native zlib and should be used when available. (PR #1850)
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Increase the input block size for bgzip. This deals with a slow down introduced in PR #1493 when reading from a pipe. (PR #1768, fixes #1767. Reported by Konstantin Riege)
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Allow BYTE_ARRAY_STOP to work on non-zero STOP code with TOK3. Although the htscodecs name tokeniser uses a NUL between names there is no reason why another value could not be used. This change lets CRAM recognise other separator values. (PR #1871)
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Remove cram seek ability to do range queries via SEEK_CUR. A probable misfeature from the original implementation. (PR #1878, fixes #1877. Reported by Rick Wertenbroek)
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Add hts_tpool_worker_id() API. This may be used to associate data with a thread rather than to a job. (PR #1875)
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Update bcf_synced_reader to use htsFile. (PR #1868, implements #1862. Requested by Brent Pedersen)
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Exit with return value 1 on tabix parse error. This previously returned 0. (PR #1887, fixes #1885. Reported by Fan-iX)
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Automatically recognise BED vs TSV files and add the option -C, --coords to set index positions (1 or 0 based coordinates) in annot-tsv. (PR #1894)
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Reading SQ lines with multiple differing LN will now fail. Such lines are invalid (by the spec) and previous handling was inconsistent. (PR #1882, fixes #1866)
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Return errors instead of EOF after all I/O errors etc in hts_itr_multi_next/sam_itr_next/sam_read1/vcf_parse/bcf_read. (PR #1899. Thanks to John Marshall)
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Remove UR:file:// and UR:ftp:// from ref search path, plus REF_PATH to EBI. Removing EBI as the default fallback when REF_PATH not set prevents the unintended DDOS on EBI's servers. (PR #1881. PR #1915, fixes oss-fuzz issue 418125747)