4.1.1

[droazen]

Bug fix and maintenance

Important CRAM writing bug fix

A serious bug which can cause corrupted reads in CRAM files was discovered and fixed in this release. This bug was introduced in HTSJDK 3.0.0, and affects Picard versions 2.27.3 through 3.1.1 and GATK versions 4.3 through 4.5.

The bug occurs in cases where there is a read aligned starting at exactly position 1 on a reference contig. This means that the bug doesn't generally impact human autosome and X/Y contigs because they tend to start with a large number of N bases and reads are not aligned at exactly position 1. The exceptions to this would be T2T references and things like mitochondrial calling.

For more information on the conditions that trigger this bug, see this post.

GATK 4.6 includes a tool called CRAMIssue8768Detector that can scan a CRAM file and report whether it is affected, and if so which regions in the file are corrupt. If you suspect that some of your CRAM files may have been affected, please run this tool on them for confirmation!

See also #1708 for more information.

What's Changed

• Fix CRAMReferenceRegion updating. by @cmnbroad in Fix CRAMReferenceRegion updating. #1708
• Updating tests in SAMRecordUnitTest to remove ambiguity by @lbergelson in Updating tests in SAMRecordUnitTest to remove ambiguity #1696
• Update to gradle 8.5 by @lbergelson in Update to gradle 8.5 #1697
• Updating our dependencies to the the newest version by @lbergelson in Updating our dependencies to the the newest version #1699
• Upgrade to samtools 1.19.1 for interop testing. by @cmnbroad in Upgrade to samtools 1.19.1 for interop testing. #1706

Full Changelog: 4.1.0...4.1.1

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This discussion was created from the release 4.1.1.