4.2.0

This is a small release with a few API additions and bug fixes. The biggest additions are the codec necessary to implement CRAM 3.1 support. It includes new CRAM codecs, however they are not yet integrated into the CRAM Reader/Writer. Support for reading Cram 3.1 should follow in the next release.

What's Changed

• Update commons compress to a 1.26.0 by @lbergelson in #1720
• Add ReferenceSequenceFile.getSubsequenceAt(final Locatable locatable) @lindenb in #1725
• Treat vcf.bgz as a valid vcf extension in FileExtensions by @lindenb in #1727
• GFF improvments: make Gff3BaseData Locatable, add 'Optional getAttr(key)' and 'hasAttribute' by @lindenb in #1726
• Improve list format in README.md by @ArtoriaZhang in #1731
• Fix ambiguity in SamUtils PairOrientation about reads needing to map to the same contig by @yfarjoun in #1709
• Minor updates to MemoryMappedFileBuffer by @lbergelson in #1700
• Update install samtools by @lbergelson in #1735
• Update github actions to use upload_artifact@4 by @lbergelson in #1734
• Implementation of CRAM 3.1 codecs. by @cmnbroad in #1714
• Set mapq on supplemental alignments in SamPairUtil by @nh13 in #1737

New Contributors

• @ArtoriaZhang made their first contribution in #1731

Full Changelog: 4.1.3...4.2.0