[ADAM-1679] Unmapped items should not get caught in requirement when …

…sorting. Resolves #1679.
bigdatagenomics · Aug 27, 2017 · f365b3f · f365b3f
1 parent 9b51df5
commit f365b3f
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Showing 2 changed files with 21 additions and 2 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
@@ -340,7 +340,7 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
 
       // We don't use ValidationStringency here because multimapped elements
       // break downstream methods.
-      require(coveredRegions.size == 1,
+      require(coveredRegions.size <= 1,
         "Cannot sort RDD containing a multimapped element. %s covers %s.".format(
           elem, coveredRegions.mkString(",")))
 
@@ -403,7 +403,7 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging {
 
       // We don't use ValidationStringency here because multimapped elements
       // break downstream methods.
-      require(coveredRegions.size == 1,
+      require(coveredRegions.size <= 1,
         "Cannot sort RDD containing a multimapped element. %s covers %s.".format(
           elem, coveredRegions.mkString(",")))
 

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala
@@ -1380,4 +1380,23 @@ class AlignmentRecordRDDSuite extends ADAMFunSuite {
     assert(htsjdkPg.getProgramVersion === "1")
     assert(htsjdkPg.getPreviousProgramGroupId === "ppg")
   }
+
+  sparkTest("GenomicRDD.sort does not fail on unmapped reads") {
+    val inputPath = testFile("unmapped.sam")
+    val reads: AlignmentRecordRDD = sc.loadAlignments(inputPath)
+    assert(reads.rdd.count === 200)
+
+    val sorted = reads.sort(stringency = ValidationStringency.SILENT)
+    assert(sorted.rdd.count === 102)
+  }
+
+  sparkTest("GenomicRDD.sortLexicographically does not fail on unmapped reads") {
+    val inputPath = testFile("unmapped.sam")
+    val reads: AlignmentRecordRDD = sc.loadAlignments(inputPath)
+    assert(reads.rdd.count === 200)
+
+    val sorted = reads.sortLexicographically(
+      stringency = ValidationStringency.SILENT)
+    assert(sorted.rdd.count === 102)
+  }
 }