[ADAM-1099] Make reference region not throw NPE.

Resolves bigdatagenomics#1099.
fnothaft · Aug 14, 2016 · fd1b6b4 · fd1b6b4
1 parent 273d57f
commit fd1b6b4
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Showing 2 changed files with 19 additions and 9 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
@@ -81,15 +81,10 @@ object ReferenceRegion {
    */
   def opt(record: AlignmentRecord): Option[ReferenceRegion] = {
     if (record.getReadMapped) {
-      Some(
-        ReferenceRegion(
-          record.getContigName,
-          record.getStart,
-          record.getEnd
-        )
-      )
-    } else
+      Some(apply(record))
+    } else {
       None
+    }
   }
 
   /**
@@ -117,6 +112,12 @@ object ReferenceRegion {
   }
 
   def apply(record: AlignmentRecord): ReferenceRegion = {
+    require(record.getReadMapped,
+      "Cannot build reference region for unmapped read %s.".format(record))
+    require(record.getContigName != null &&
+      record.getStart != null &&
+      record.getEnd != null,
+      "Read %s contains required fields that are null.".format(record))
     ReferenceRegion(record.getContigName, record.getStart, record.getEnd)
   }
 

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
@@ -122,14 +122,23 @@ class ReferenceRegionSuite extends FunSuite {
   }
 
   test("create region from unmapped read fails") {
-    intercept[NullPointerException] {
+    intercept[IllegalArgumentException] {
       val read = AlignmentRecord.newBuilder()
         .setReadMapped(false)
         .build()
       ReferenceRegion(read)
     }
   }
 
+  test("create region from read with null alignment positions fails") {
+    intercept[IllegalArgumentException] {
+      val read = AlignmentRecord.newBuilder()
+        .setReadMapped(true)
+        .build()
+      ReferenceRegion(read)
+    }
+  }
+
   test("create region from mapped read contains read start and end") {
     val read = AlignmentRecord.newBuilder()
       .setReadMapped(true)