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A Picard-style .interval_list file is a feature file, but FeatureManager.isFeatureFile also checks its existence, which means a feature file path that is missing gets (unsuccessfully) parsed as an interval string literal and throws a misleading exception:
org.broadinstitute.hellbender.exceptions.UserException$MalformedGenomeLoc: Badly formed genome unclippedLoc: Query interval "missing_file.interval_list" is not valid for this input.
This should be a quick fix, I just don't want to add more to the PR I'm working on.
The text was updated successfully, but these errors were encountered:
A Picard-style .interval_list file is a feature file, but FeatureManager.isFeatureFile also checks its existence, which means a feature file path that is missing gets (unsuccessfully) parsed as an interval string literal and throws a misleading exception:
org.broadinstitute.hellbender.exceptions.UserException$MalformedGenomeLoc: Badly formed genome unclippedLoc: Query interval "missing_file.interval_list" is not valid for this input.
This should be a quick fix, I just don't want to add more to the PR I'm working on.
The text was updated successfully, but these errors were encountered: