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@lbergelson lbergelson released this 19 Feb 21:01
· 125 commits to master since this release
2.21.2
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lbergelson Louis Bergelson
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Learn about vigilant mode.
5445b90
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Learn about vigilant mode.

This is a small release with several new features and bug fixes.

This release is compatible with 2.21.1

New features:

  • New codec for reading GFF3 files (#1439). Htsjdk can now read General Feature Format files and produce Gff3Features. The GFF allows encoding complex Genomic annotations and features, like transcripts annotations, gene sets, exonic regions, etc. This is a fairly complex file type, so please let us know if you encounter any issues, or if you are interested in reading files with directives that are not yet supported in htsjdk. This code is subject to change over the next few releases if we encounter significant issues.

  • The codec for interval list files now recognizes compressed .interval_list.gz files (#1458)

Complete Change List:

5445b90 SamSequenceRecord implements Locatable (#1459)
4e1363f support interval_list with gz compression (#1458)
051db91 TabixReader implements Autoclose (#1457)
bfb584e Modified numLikelihoods calculation for performance (#1447)
acf2d51 new Gff3 Tribble Codec (#1439)
75086d1 Made toIntervalList an iterator as well ... (#1455)
5a9a1ed fix resource leak in VCFFileReader.getSequenceDictionary(#1451)
5b47e37 Fix IndexFactory on non-default file system. (#1449)
3df5a35 Cleanup temp files after encountering an exception in SAMFileWriter(#1444)
a240a11 Upgrade to samtools 1.10. (#1443)

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