Add end-to-end test for BQSR

bigdatagenomics · Mar 11, 2014 · 5f73312 · 5f73312
1 parent 3b68675
commit 5f73312
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Showing 5 changed files with 2,286 additions and 9 deletions.
diff --git a/...c/main/scala/edu/berkeley/cs/amplab/adam/rdd/recalibration/BaseQualityRecalibration.scala b/...c/main/scala/edu/berkeley/cs/amplab/adam/rdd/recalibration/BaseQualityRecalibration.scala
@@ -54,22 +54,18 @@ extends Serializable with Logging {
   // TODO: parameterize
   val minAcceptableQuality = QualityScore(5)
 
-  // Compute and apply recalibration
-  def apply(): RDD[ADAMRecord] = {
+  val observed: ObservationTable = {
     def shouldIncludeRead(read: DecadentRead) =
       read.isCanonicalRecord &&
         read.alignmentQuality.exists(_ > QualityScore.zero) &&
         read.passedQualityChecks
 
-    // First phase
-    val observed: ObservationTable = reads.
+    reads.
       filter(shouldIncludeRead).flatMap(observe).
       aggregate(ObservationAccumulator(covariates))(_ += _, _ ++= _).result
+  }
 
-    // Log the ObservationTable (for debugging and generating plots)
-    //println(observed.toCSV)
-
-    // Second phase
+  val result: RDD[ADAMRecord] = {
     val recalibrator = Recalibrator(observed, minAcceptableQuality)
     reads.map(recalibrator)
   }
@@ -94,6 +90,6 @@ extends Serializable with Logging {
 object BaseQualityRecalibration {
   def apply(rdd: RDD[ADAMRecord], knownSnps: SnpTable): RDD[ADAMRecord] = {
     val sc = rdd.context
-    new BaseQualityRecalibration(cloy(rdd), sc.broadcast(knownSnps)).apply()
+    new BaseQualityRecalibration(cloy(rdd), sc.broadcast(knownSnps)).result
   }
 }