Merge pull request #22 from bigdatagenomics/matt-sorttest

Add a unit test for sorting reads

adam-commands/src/test/scala/edu/berkeley/cs/amplab/adam/rdd/AdamRDDFunctionsSuite.scala

@@ -16,10 +16,10 @@
 package edu.berkeley.cs.amplab.adam.rdd
 
 import org.apache.spark.rdd.RDD
-import edu.berkeley.cs.amplab.adam.avro.{ADAMPileup, Base}
+import edu.berkeley.cs.amplab.adam.avro.{ADAMRecord, ADAMPileup, Base}
 import edu.berkeley.cs.amplab.adam.util.SparkFunSuite
 import edu.berkeley.cs.amplab.adam.rdd.AdamContext._
-import edu.berkeley.cs.amplab.adam.models.ADAMRod
+import scala.util.Random
 
 class AdamRDDFunctionsSuite extends SparkFunSuite {
 
@@ -163,4 +163,26 @@ class AdamRDDFunctionsSuite extends SparkFunSuite {
  assert(coverage > 1.99 && coverage < 2.01)
  }
 
+ sparkTest("sorting reads") {
+ val random = new Random("sorting".hashCode)
+ val numReadsToCreate = 1000
+ val reads = for (i <- 0 until numReadsToCreate) yield {
+ val mapped = random.nextBoolean()
+ val builder = ADAMRecord.newBuilder().setReadMapped(mapped)
+ if (mapped) {
+ builder.setReferenceId(random.nextInt(numReadsToCreate / 10)).setStart(random.nextInt(1000000))
+ }
+ builder.build()
+ }
+ val rdd = sc.parallelize(reads)
+ val sortedReads = rdd.adamSortReadsByReferencePosition().collect().zipWithIndex
+ val (mapped, unmapped) = sortedReads.partition(_._1.getReadMapped)
+ // Make sure that all the unmapped reads are placed at the end
+ assert(unmapped.forall(p => p._2 > mapped.takeRight(1)(0)._2))
+ // Make sure that we appropriately sorted the reads
+ val expectedSortedReads = mapped.sortWith(
+ (a, b) => a._1.getReferenceId < b._1.getReferenceId && a._1.getStart < b._1.getStart)
+ assert(expectedSortedReads === mapped)
+ }
+
 }