RAW_MQ/sumSquaredMQs parsing error when running GenotypeGVCFs for JointGenotyping

[indraniel]

This issue affect version of GATK4 from version 4.0.10.1 and onwards, and is related to github feature/pull request #4969: "Improve MQ calculation accuracy".

GVCFs with large RAW_MQ sum of sumSquaredMQs values end up with an error like:

A USER ERROR has occurred: Bad input: malformed RAW_MQ annotation: 3415207168,1749038

The error happens when the sumSquaredMQs element value is greater than Java's. Integer.MAX_VALUE. See the following github pull request comment for more details.

Should a java.lang.Long, java.math.BigInteger, java.lang.Double, or java.math.BigDecimal be used here instead of a java.lang.Integer for method: parseRawDataString inside org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality ?

I've noticed this error when using GATK4 version 4.0.11.0 on the GATK4 Germline SNPs-INDELs WDL workflow. It happens on the JointGenotyping.GenotypeGVCFs task.

[indraniel]

Looks like the work in pull request 5435 is related to this issue.

[TedBrookings]

Yes, I messed up the commit message and wrote that it "resolves issue 5433" instead of "resolves issue #5433". Without the hash I guess github assumes it's stupid meatbag language and ignores it. The bug should be fixed so I'm closing the issue manually. Sorry to leave this hanging the last month, and thanks for pointing it out.

[indraniel]

No worries! Thanks again for the fix!