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Use htsjdk getAttributeAsList for VCF INFO ANN key #1348

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merged 2 commits into from Jan 16, 2017

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heuermh commented Jan 10, 2017

Fixes #1347

For review; I'll push additional commit(s) to this pull request with more unit tests later.

@heuermh heuermh modified the milestones: 0.21.1, 0.22.0 Jan 10, 2017

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Test PASSed.
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@fnothaft

1 small nit, otherwise LGTM!

try {
attrOpt.flatMap(attr => parseAndFilter(attr))
attrOpt.flatMap(attr => parseAndFilter(attr.asScala.map(_.asInstanceOf[java.lang.String])))

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fnothaft Jan 10, 2017

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You shouldn't need the _.asInstanceOf here, as scala's String == java.lang.String.

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fnothaft Jan 10, 2017

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You shouldn't need the _.asInstanceOf here, as scala's String == java.lang.String.

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heuermh Jan 10, 2017

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the list wrapped by the option is java.util.List[Object] because fuck you, htsjdk

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heuermh Jan 10, 2017

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the list wrapped by the option is java.util.List[Object] because fuck you, htsjdk

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fnothaft Jan 10, 2017

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Oh, that's right. HOT DIGGITY DOG!

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fnothaft Jan 10, 2017

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Oh, that's right. HOT DIGGITY DOG!

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fnothaft Jan 10, 2017

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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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fnothaft Jan 10, 2017

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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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heuermh Jan 10, 2017

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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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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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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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heuermh commented Jan 16, 2017

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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LGTM; thanks for ping @heuermh

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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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fnothaft commented Jan 16, 2017

I'm going to merge this; if we find any problems on ExAC on GRCh38, we can revise in a later PR.

@fnothaft fnothaft merged commit 938f62a into bigdatagenomics:master Jan 16, 2017

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Merged! Thanks @heuermh!

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fnothaft commented Jan 16, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:issue-1374 branch Jan 16, 2017

@majkiw

Hey, sorry, I didn't know I had reviewer rights :)
It looks great - thank you @heuermh and @fnothaft
I am leaving a nitpicking comment as a proof I read it.

@@ -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"))
}
def toObjectList(values: String*): java.util.List[Object] = {

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majkiw Jan 17, 2017

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I think this could be replaced with java.util.Arrays.asList[Object](values)

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majkiw Jan 17, 2017

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I think this could be replaced with java.util.Arrays.asList[Object](values)

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