BQSR using vcf loader #180
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All automated tests passed. |
| @@ -73,4 +72,12 @@ object SnpTable { | |||
| // construct SnpTable from immutable copy of `table` | |||
| new SnpTable(table.mapValues(_.toSet).toMap) | |||
| } | |||
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| def apply(variants : RDD[RichADAMVariant]) : SnpTable = | |||
| { | |||
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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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Thanks for making this change, @arahuja! |
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All automated tests passed. |
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Merged! Thanks @arahuja! |
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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.