[ADAM-369] Improve debug output for indel realigner #369
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| (r.mdTag.get.getReference(r), r.getStart.toLong to r.getEnd) | ||
| val readRefs = reads.flatMap((r: RichAlignmentRecord) => { | ||
| if (r.mdTag.isDefined) { | ||
| Some((r.mdTag.get.getReference(r), r.getStart.toLong to r.getEnd)) |
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Isn't this doing a get and then re-wrapping the tuple in an option? Maybe:
mdTag.map( tag => (tag, r.getStart.toLong to r.getEnd))instead of the isDefined + get
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I print a warning and log some data in the else clause. If I didn't have the else clause, I would agree. I think I could change this to a fold, but I'm not sure if that'd be much cleaner.
fnothaft
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This is rebased on master. |
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Can you rebase again, @fnothaft ? |
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Rebased. |
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LGTM, thanks @fnothaft! |
tdanford
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[ADAM-369] Improve debug output for indel realigner
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Addresses bug reported on mailing list with output in this gist.
The indel realigner was trying to read the MD tag on a read that did not have an MD tag attached. To address this, I've: