wrote getPairOrientation method for GATKRead #6420
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sorry, David, just noticed this. |
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@SHuang-Broad |
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Sorry to be a bug, @davidbenjamin , (and a late one) but have you considered the following scenario?
It may be worth it to check for "improperly paired" flag, then.
src/main/java/org/broadinstitute/hellbender/utils/read/GATKRead.java
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src/test/java/org/broadinstitute/hellbender/utils/read/GATKReadAdaptersUnitTest.java
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| reverseStrandTandem.setMateIsReverseStrand(true); | ||
| reverseStrandTandem.setPosition(new SimpleInterval("1", 100, 200)); | ||
| reverseStrandTandem.setMatePosition(new SimpleInterval("1", 200, 300)); | ||
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May I also suggest adding test cases:
- mates mapped to different chromosomes
Of course if you believe getting pair orientation from such mate pairs to be non-sense, then it should be move to the test cases expecting exceptions.
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@SHuang-Broad What's your opinion? It doesn't seem like any of the existing values of SamPairUtil.PairOrientation make sense. If it weren't in htsjdk I would be tempted to add DIFFERENT_CHROMOSOMES to the enum. I could imagine throwing an error and leaving it to the calling code to check. I could also imagine having this method return an Optional<SamPairUtil.PairOrientation> and reserving an empty result for this case.
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@SHuang-Broad Could you explain your disperse duplicated / improperly paired scenario? It seems to me that if a read and its mate map to the same strand then they have to be oriented in the same (5-prime to 3-prime) direction. I quickly looked into the improperly paired flag and the word online is that there's no fixed definition. Sometimes it just means an innie with larger-than-expected fragment size. I will do whatever you want me to do, because I'm just trying to close old GATK issues! |
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Yes, we need to talk and draw on a board when we are both in office. It's a bit hard to explain via pure text here. |
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Sounds good! |
Closes #1550. @SHuang-Broad do you still want this?