[ADAM-776] Rename duplicate OUTPUT metaVar in ADAM2Fastq.

Resolves #776.

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala

@@ -28,16 +28,21 @@ import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4JOption }
 
 class ADAM2FastqArgs extends ParquetLoadSaveArgs {
- @Argument(required = false, metaVar = "OUTPUT", usage = "When writing FASTQ data, all second-in-pair reads will go here, if this argument is provided", index = 2)
+ @Argument(required = false, metaVar = "SECOND_OUTPUT", usage = "When writing FASTQ data, all second-in-pair reads will go here, if this argument is provided", index = 2)
  var outputPath2: String = null
+
  @Args4JOption(required = false, name = "-validation", usage = "SAM tools validation level; when STRICT, checks that all reads are paired.")
  var validationStringency = ValidationStringency.LENIENT
+
  @Args4JOption(required = false, name = "-repartition", usage = "Set the number of partitions to map data to")
  var repartition: Int = -1
+
  @Args4JOption(required = false, name = "-persist_level", usage = "Persist() intermediate RDDs")
  var persistLevel: String = null
+
  @Args4JOption(required = false, name = "-no_projection", usage = "Disable projection on records. No great reason to do this, but useful for testing / comparison.")
  var disableProjection: Boolean = false
+
  @Args4JOption(required = false, name = "-output_oq", usage = "Output the original sequencing quality scores")
  var outputOriginalBaseQualities = false
 }