Adding rod functionality: a specialized grouping of pileup data. #21
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I'm changing something in the tests — please don't merge yet. |
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OK — this is good to roll now. |
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| @@ -26,7 +26,7 @@ import org.apache.spark.SparkContext | |||
| import org.apache.spark.rdd.RDD | |||
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| object PileupAggregator extends AdamCommandCompanion { | |||
| val commandName: String = "aggregate_pileups" | |||
| val commandName: String = "aggregatePileups" | |||
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Command-line names with capitalization should be avoided. Maybe use "paggregate" or "pagg" to make it easier to type?
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| // all bases must be at the same position | ||
| require(pileups.forall(_.getPosition.toLong == position)) | ||
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| lazy val singleSample: Boolean = pileups.map(_.getRecordGroupSample).distinct.length == 1 |
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boolean values/method usually start with "is", e.g. isSingleSample. Having singleSample alone might imply to another developer that it's a way to get a singleSample.
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I just noticed you have 'isSingleSample' below. Any reason to not just rename the val and drop the def?
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Other than the small Boolean nit above, I think this is ready to ship. Thanks, Frank! |
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The boolean nit is fixed now. |
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Jenkins, test this please. |
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Adding rod functionality: a specialized grouping of pileup data.
Rods group all pileup data at a specific point on the locus — this commit provides a clean container for this data, as well as methods for performing conversion from pileups to rods.