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VariantContext converter refactor #175

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arahuja
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@arahuja arahuja commented Mar 15, 2014

This PR doesn't add any new functionality but just some cleanup/refactor on VariantContextConverter. This is a precursor of PR #173, but I pulled it out separately.

  • Move INFO field parsing of annotation to VariantAnnotationConverter
  • Broke genotype and variant parsing to separate functions
  • Delete repeated functions
  • Change underscore to camel case

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/220/

}
private def attrAsString(attr: Object):Object = attr match {
case a: String => a
case a: java.util.List[String] => a(0)
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I had a question RE: this line in #175.

@fnothaft
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This should merge before #173, correct?

@arahuja
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arahuja commented Mar 17, 2014

Yes, this would come before #173. #173 actually has the new annotation parsing, while this is just some cleanup to enable that

@arahuja
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arahuja commented Mar 17, 2014

From the comments in the other one, I fixed braces and removed the array to string conversion

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Excellent! If you can squash this down, I think it is ready to merge.

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/227/

fnothaft added a commit that referenced this pull request Mar 17, 2014
@fnothaft fnothaft merged commit 59b8210 into bigdatagenomics:master Mar 17, 2014
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Merged! Thanks @arahuja!

@arahuja arahuja deleted the variant-converter-refactor branch March 17, 2014 21:10
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3 participants