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Refactor/mark buckets #2015

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jondeaton commented Jul 13, 2018

The leftPositionAndLibrary function in markBuckets was a bit hard to understand. This PR refactors it so that it is easier to understand and also so that it uses Option(None) instead of null. Also minor documentation fix.

@@ -96,14 +94,20 @@ private[rdd] object MarkDuplicates extends Serializable with Logging {
recordGroups: RecordGroupDictionary): RDD[SingleReadBucket] = {
checkRecordGroups(recordGroups)

// Gets the library of a SingleReadBucket
def getLibrary(singleReadBucket: SingleReadBucket): Option[String] = {

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jondeaton Jul 13, 2018

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It might also be better to make library a method of SingleReadBucket to replace this getLibrary function.

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AmplabJenkins commented Jul 13, 2018

Can one of the admins verify this patch?

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heuermh commented Jul 13, 2018

Jenkins, test this please

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heuermh commented Jul 13, 2018

Jenkins, add to whitelist

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coveralls commented Jul 13, 2018

Coverage Status

Coverage increased (+0.04%) to 78.977% when pulling 357bdea on jondeaton:refactor/markBuckets into 8e8007e on bigdatagenomics:master.

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coveralls commented Jul 13, 2018

Coverage Status

Coverage increased (+0.04%) to 78.977% when pulling 357bdea on jondeaton:refactor/markBuckets into 8e8007e on bigdatagenomics:master.

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coveralls commented Jul 13, 2018

Coverage Status

Coverage increased (+0.04%) to 78.977% when pulling 357bdea on jondeaton:refactor/markBuckets into 8e8007e on bigdatagenomics:master.

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AmplabJenkins commented Jul 13, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2785/
Test PASSed.

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