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IntervalUtils::loadIntervals gives bad error on missing .interval_list file #6956

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ldgauthier opened this issue Nov 13, 2020 · 0 comments
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Engine learn GATK Suitable for GATK beginners

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@ldgauthier
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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.

@droazen droazen added the Engine label Nov 23, 2020
@droazen droazen added the learn GATK Suitable for GATK beginners label Aug 24, 2021
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