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ValidationStringency in MDTagging should apply to reads on unknown references #1365

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fnothaft opened this Issue Jan 23, 2017 · 0 comments

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fnothaft commented Jan 23, 2017

Right now, if you have a read that is mapped to an unknown reference contig (not provided in reference build) when you are recomputing MD tags, it throws an exception. This makes sense, but we should be able to suppress these exceptions with ValidationStringency (i.e., if the read is mapped to a decoy contig), which is already passed in to MdTagging.

@fnothaft fnothaft added this to the 0.22.0 milestone Jan 23, 2017

@fnothaft fnothaft self-assigned this Jan 23, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Jan 23, 2017

[ADAM-1365] Apply validation stringency to reads on missing contigs w…
…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.

@heuermh heuermh closed this in #1366 Jan 23, 2017

heuermh added a commit that referenced this issue Jan 23, 2017

[ADAM-1365] Apply validation stringency to reads on missing contigs w…
…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.

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

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