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When I try to run the latest version of the DataProcessingPipeline I get the following error message:
However in the recal case class this option is set to be true:
this.disable_indel_quals = true
Any idea how to solve this? It seams to me this is a bug, but I cannot find the source for the PrintReads class (guessing that its not in the public code), so I can't check it myself.