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[ADAM-1365] Apply validation stringency to reads on missing contigs when MD tagging #1366

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@fnothaft
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@fnothaft fnothaft commented Jan 23, 2017

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.

…hen MD tagging

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.
@fnothaft fnothaft added this to the 0.22.0 milestone Jan 23, 2017
.extract(ReferenceRegion.unstranded(read)))
} catch {
case t: Throwable => {
if (validationStringency == ValidationStringency.STRICT) {

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@heuermh

heuermh Jan 23, 2017
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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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@fnothaft

fnothaft Jan 23, 2017
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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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@heuermh

heuermh Jan 23, 2017
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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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@AmplabJenkins AmplabJenkins commented Jan 23, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1750/
Test PASSed.

@heuermh heuermh merged commit c0ed2b2 into bigdatagenomics:master Jan 23, 2017
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@heuermh heuermh commented Jan 23, 2017

Thank you, @fnothaft!

@heuermh heuermh added this to Completed in Release 0.23.0 Mar 8, 2017
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