Silently missing values when using integer format in rank model and encountering a float value

[Jakob37]

We had an issue where some GATK only structural variants did not obtain a rank score.

Looking closer, we found that we had mistakenly specified "integer" as format on GATKs quality GQC field and specified integer ranges.

Some of the GATK GQC values were actually floats. These silently got no rank scores.

It would be useful to get complaints from Genmod when encountering values of formats outside those written in the rank model.

I wanted to share the info as it might save someone else some headache.

[henrikstranneheim]

Thanks for the feedback. Our main developer is currently on parental leave until the fall. So this'll probably be on hold until then. We are also focusing our efforts creating a new app which will replace genmod and use more sophisticated prioritization models.

[Jakob37]

Thanks for the feedback. Our main developer is currently on parental leave until the fall. So this'll probably be on hold until then. We are also focusing our efforts creating a new app which will replace genmod and use more sophisticated prioritization models.

I see, thanks for the information!