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BQSR using vcf loader #180

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merged 1 commit into from
Mar 17, 2014
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arahuja
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@arahuja arahuja commented Mar 17, 2014

Changes BQSR command to use standard VCF loading process as opposed to separate parser. I left in the other way as another option, but we can remove it as well.

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One or more automated tests failed
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/230/

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/232/

@@ -73,4 +72,12 @@ object SnpTable {
// construct SnpTable from immutable copy of `table`
new SnpTable(table.mapValues(_.toSet).toMap)
}

def apply(variants : RDD[RichADAMVariant]) : SnpTable =
{
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Nit: braces style.

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Ugh, clearly picked this habit up somewhere and can't break it. Will fix.

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No prob; I write all my C++ code this way, so I can relate...

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I had one small nit, otherwise this looks good to merge.

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jey commented Mar 17, 2014

Thanks for making this change, @arahuja!

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/233/

fnothaft added a commit that referenced this pull request Mar 17, 2014
@fnothaft fnothaft merged commit add948d into bigdatagenomics:master Mar 17, 2014
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Merged! Thanks @arahuja!

@hammer hammer deleted the bqsr-vcf branch March 18, 2014 15:55
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4 participants