htslib release 1.15: Features and Updates -------------------- * Bgzip now has a --keep option to not remove the input file after compressing. (PR#1331) * Improved file format detection so some BED files are no longer detected as FASTQ or FASTA. (PR#1350, thanks to John Marshall) * Added xz (lzma), zstd and D4 formats to the file type detection functions. We don't actively support reading these data types, but function calls and htsfile can detect them. (PR#1340, thanks to John Marshall) * CRAM now also uses libdeflate for read-names if the libdeflate version is new enough (1.9 onwards). Previously we used zlib for this due to poor performance of libdeflate. This gives a slight speed up and reduction in file size. (PR#1383) * The VCF and BCF readers will now issue a warning if contig, INFO or FORMAT IDs do not match the formats described in the VCFv4.3 specification. Note that while the invalid names will mostly still be accepted, future updates will convert the warnings to errors causing files including invalid names to be rejected. (PR#1389) Build changes ------------- These are compiler, configuration and makefile based changes. * HTSlib now uses libhtscodecs release 1.2.1. * Improved support for compiling and linking against HTSlib with Microsoft Visual Studio. (PR#1380, #1377, #1375. Thanks to Aidan Bickford and John Marshall) * Various internal CI improvements. Bug fixes --------- * Fixed CRAM index queries for HTSJDK output (PR#1388, reported by Chris Norman). Note this also fixes writing CRAM writing, to match the specification (and HTSJDK), from version 3.1 onwards. * Fixed CRAM index queries when required-fields settings are selected to ignore CIGARs (PR#1372, reported by Giulio Genovese). * Unmapped but placed (having chr/pos) are now included in the BAM indices. (PR#1352, thanks to John Marshall) * CRAM now honours the filename##idx##index nomenclature for specifying non-standard index locations. (PR#1360, reported by Michael Cariaso) * Minor CRAM v1.0 read-group fix (PR#1349, thanks to John Marshall) * Permit .fa and .fq file type detection as synonyms for FASTA and FASTQ. (PR#1386). * Empty VCF format fields are now output ":.:" as instead of "::". (PR#1370) * Repeated bcf_sr_seek calls now work. (PR#1363, reported by Giulio Genovese) * Bcf_remove_allele_set now works on unpacked BCF records. (PR#1358, reported by Brent Pedersen). * The hts_parse_decimal() function used to read numbers in region lists is now better at rejecting non-numeric values. In particular it now rejects a lone 'G' instead of interpreting it as '0G', i.e. zero. (PR#1396, PR#1400, reported by SSSimon Yang; thanks to John Marshall). * Improve support for GPU issues listed by -Wdouble-promotion. (PR#1365, reported by David Seisert) * Fix example code in header file documentation. (PR#1381, Thanks to Aidan Bickford)