Use htsjdk getAttributeAsList for VCF INFO ANN key #1348
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Test PASSed. |
| try { | ||
| attrOpt.flatMap(attr => parseAndFilter(attr)) | ||
| attrOpt.flatMap(attr => parseAndFilter(attr.asScala.map(_.asInstanceOf[java.lang.String]))) |
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You shouldn't need the _.asInstanceOf here, as scala's String == java.lang.String.
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the list wrapped by the option is java.util.List[Object] because fuck you, htsjdk
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Oh, that's right. HOT DIGGITY DOG!
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Well, I guess we're good here then. You said you've got more tests coming, right?
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Yeah I will have higher level ones that read from SnpEff-annotated VCF files, need to get back to the other laptop
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Test PASSed. |
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Ping @majkiw @jpdna @fnothaft for review, merge. I'd like to use ExAC lifted over to GRCh38 for further testing and this is a blocker. |
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I'm going to merge this; if we find any problems on ExAC on GRCh38, we can revise in a later PR. |
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Merged! Thanks @heuermh! |
| @@ -310,4 +389,10 @@ class TranscriptEffectConverterSuite extends ADAMFunSuite { | |||
| // when ValidationStringency is made available for --> VCF, test STRICT throws exception | |||
| assert(!TranscriptEffectConverter.convertToVcfInfoAnnValue(Seq(te)).contains("2")) | |||
| } | |||
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| def toObjectList(values: String*): java.util.List[Object] = { | |||
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I think this could be replaced with java.util.Arrays.asList[Object](values)
Fixes #1347
For review; I'll push additional commit(s) to this pull request with more unit tests later.