[ADAM-1365] Apply validation stringency to reads on missing contigs when MD tagging #1366
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…hen MD tagging Resolves bigdatagenomics#1365. If a read is mapped to a contig that is missing from the broadcasted fragment map, we look at the user's provided validation stringency before throwing an exception.
| .extract(ReferenceRegion.unstranded(read))) | ||
| } catch { | ||
| case t: Throwable => { | ||
| if (validationStringency == ValidationStringency.STRICT) { |
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The more we use ValidationStringency outside of forwarding to htsjdk, the less I like using their enum.
I know this isn't the place; what do you think of an ADAM-specific enum that maps to ValidationStringency where necessary? We could use the opportunity to come up with a better name, since it isn't really about validation, it is more about error reporting.
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I'm +0. I don't love ValidationStringency, but I'm a bit too lazy to deconvolve it from our codebase. I guess I'd say that it is on the sorted list of refactors that I'd like to do, but lower down on the list. That being said, it's probably not that much work. CC @ryan-williams for thoughts as well.
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Yeah that's where I'm at too. If I had a better name ready, I'd do it.
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Test PASSed. |
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Thank you, @fnothaft! |
Resolves #1365. If a read is mapped to a contig that is missing from the broadcasted fragment map, we look at the user's provided validation stringency before throwing an exception.