broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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AD values in Annotation aren't Integers #663

Open MattWellie opened 6 months ago

MattWellie commented 6 months ago

Relates to #661

This issue is better explained there - as far as I can see the AD processing script includes the possibility of generating float values for an Integer field, which causes the pysam handler to raise an exception.

  1. Am I interpreting this error mode correctly? It seems like the odds of nobody ever having run into this before are wildly unlikely, but the errors I am deterministically seeing now make sense if this is a bug in the code
  2. If so, can we replace this with a floor division (//) or int() wrapper so that we only ever populate ints into the Integer field