[ADAM-1486] Respect validation stringency if BAM header load fails.

Resolves #1486.
bigdatagenomics · May 12, 2017 · bbc8638 · bbc8638
1 parent 18191f9
commit bbc8638
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Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -595,9 +595,13 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
             Some((sd, rg))
           } catch {
             case e: Throwable => {
-              log.error(
-                s"Loading failed for $fp:n${e.getMessage}\n\t${e.getStackTrace.take(25).map(_.toString).mkString("\n\t")}"
-              )
+              if (validationStringency == ValidationStringency.STRICT) {
+                throw e
+              } else if (validationStringency == ValidationStringency.LENIENT) {
+                log.error(
+                  s"Loading failed for $fp:\n${e.getMessage}\n\t${e.getStackTrace.take(25).map(_.toString).mkString("\n\t")}"
+                )
+              }
               None
             }
           }

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
@@ -17,6 +17,7 @@
  */
 package org.bdgenomics.adam.rdd
 
+import htsjdk.samtools.{ SAMFormatException, ValidationStringency }
 import java.io.{ File, FileNotFoundException }
 import com.google.common.io.Files
 import org.apache.hadoop.fs.Path
@@ -81,6 +82,13 @@ class ADAMContextSuite extends ADAMFunSuite {
     assert(reads.count() === 20)
   }
 
+  sparkTest("loading a sam file with a bad header and strict stringency should fail") {
+    val path = testFile("badheader.sam")
+    intercept[SAMFormatException] {
+      sc.loadBam(path, validationStringency = ValidationStringency.STRICT)
+    }
+  }
+
   sparkTest("can read a small .CRAM file") {
     val path = testFile("artificial.cram")
     val referencePath = resourceUrl("artificial.fa").toString