Support validation stringency in out formatters.

bigdatagenomics · Mar 27, 2018 · 5328a8f · 5328a8f
1 parent 1bfddc6
commit 5328a8f
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Showing 4 changed files with 41 additions and 11 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.scala
@@ -30,10 +30,13 @@ import scala.collection.mutable.ListBuffer
 
 /**
  * OutFormatter that reads streaming BED format.
+ *
+ * @param stringency Validation stringency. Defaults to ValidationStringency.STRICT.
  */
-case class BEDOutFormatter() extends OutFormatter[Feature] {
+case class BEDOutFormatter(
+    val stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] {
+
   val bedParser = new BEDParser
-  val stringency = ValidationStringency.STRICT
 
   /**
    * Reads features from an input stream in BED format.

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3OutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3OutFormatter.scala
@@ -30,10 +30,13 @@ import scala.collection.mutable.ListBuffer
 
 /**
  * OutFormatter that reads streaming GFF3 format.
+ *
+ * @param stringency Validation stringency. Defaults to ValidationStringency.STRICT.
  */
-case class GFF3OutFormatter() extends OutFormatter[Feature] {
+case class GFF3OutFormatter(
+    val stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] {
+
   val gff3Parser = new GFF3Parser
-  val stringency = ValidationStringency.STRICT
 
   /**
    * Reads features from an input stream in GFF3 format.

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.scala
@@ -30,10 +30,13 @@ import scala.collection.mutable.ListBuffer
 
 /**
  * OutFormatter that reads streaming GTF format.
+ *
+ * @param stringency Validation stringency. Defaults to ValidationStringency.STRICT.
  */
-case class GTFOutFormatter() extends OutFormatter[Feature] {
+case class GTFOutFormatter(
+    val stringency: ValidationStringency = ValidationStringency.STRICT) extends OutFormatter[Feature] {
+
   val gtfParser = new GTFParser
-  val stringency = ValidationStringency.STRICT
 
   /**
    * Reads features from an input stream in GTF format.

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VCFOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VCFOutFormatter.scala
@@ -42,28 +42,49 @@ import scala.collection.mutable.ListBuffer
  * OutFormatter that reads streaming VCF.
  *
  * @param conf Hadoop configuration.
+ * @param stringency Validation stringency.
  * @param optHeaderLines Optional accumulator for VCF header lines.
  */
 case class VCFOutFormatter(
     @transient conf: Configuration,
+    val stringency: ValidationStringency,
     val optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging {
 
   private val nestAnn = VariantContextConverter.getNestAnnotationInGenotypesProperty(conf)
 
   /**
-   * OutFormatter that reads streaming VCF. Java-friendly no-arg constructor.
+   * OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT.
+   * Java-friendly no-arg constructor.
    *
    * @param conf Hadoop configuration.
    */
-  def this(conf: Configuration) = this(conf, None)
+  def this(conf: Configuration) = this(conf, ValidationStringency.LENIENT, None)
 
   /**
    * OutFormatter that reads streaming VCF. Java-friendly constructor.
    *
    * @param conf Hadoop configuration.
    * @param acc Accumulator for VCF header lines.
    */
-  def this(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine]) = this(conf, Some(acc))
+  def this(conf: Configuration, stringency: ValidationStringency) = this(conf, stringency, None)
+
+  /**
+   * OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT.
+   * Java-friendly constructor.
+   *
+   * @param conf Hadoop configuration.
+   * @param acc Accumulator for VCF header lines.
+   */
+  def this(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine]) = this(conf, ValidationStringency.LENIENT, Some(acc))
+
+  /**
+   * OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT.
+   * Java-friendly constructor.
+   *
+   * @param conf Hadoop configuration.
+   * @param optHeaderLines Optional accumulator for VCF header lines.
+   */
+  def this(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) = this(conf, ValidationStringency.LENIENT, optHeaderLines)
 
   /**
    * Reads VariantContexts from an input stream. Autodetects VCF format.
@@ -83,14 +104,14 @@ case class VCFOutFormatter(
     val header = codec.readActualHeader(lri).asInstanceOf[VCFHeader]
 
     // merge header lines with our supported header lines
-    val lines = cleanAndMixInSupportedLines(headerLines(header), ValidationStringency.LENIENT, log)
+    val lines = cleanAndMixInSupportedLines(headerLines(header), stringency, log)
 
     // accumulate header lines if desired
     optHeaderLines.map(accumulator => lines.foreach(line => accumulator.add(line)))
 
     // make converter
     val converter = new VariantContextConverter(lines,
-      ValidationStringency.LENIENT,
+      stringency,
       nestAnn)
 
     @tailrec def convertIterator(iter: AsciiLineReaderIterator,