[ADAM-1703] Expose ValidationStringency in AnySAMOutFormatter.

Resolves bigdatagenomics#1703.
fnothaft · Aug 30, 2017 · 69dcfa5 · 69dcfa5
1 parent bac6c1d
commit 69dcfa5
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
@@ -29,7 +29,7 @@ import scala.collection.mutable.ListBuffer
  * An OutFormatter that automatically infers whether the piped input is SAM or
  * BAM. Autodetecting streamed CRAM is not currently supported.
  */
-class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
+case class AnySAMOutFormatter(stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[AlignmentRecord] {
 
   /**
    * Reads alignment records from an input stream. Autodetects SAM/BAM format.
@@ -41,6 +41,7 @@ class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
 
     // make reader
     val reader = SamReaderFactory.makeDefault()
+      .validationStringency(stringency)
       .open(SamInputResource.of(is))
 
     SAMIteratorConverter(reader)