Merge pull request #792 from fnothaft/repartition-fasta

[ADAM-791] Add repartition parameter to Fasta2ADAM.
bigdatagenomics · Aug 21, 2015 · ec525d4 · ec525d4
2 parents 207eeba + 0c62f17
commit ec525d4
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala
@@ -42,6 +42,8 @@ class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs {
  var reads: String = ""
  @Args4jOption(required = false, name = "-fragment_length", usage = "Sets maximum fragment length. Default value is 10,000. Values greater than 1e9 should be avoided.")
  var fragmentLength: Long = 10000L
+ @Args4jOption(required = false, name = "-repartition", usage = "Sets the number of output partitions to write, if desired.")
+ var partitions: Int = -1
 }
 
 class Fasta2ADAM(protected val args: Fasta2ADAMArgs) extends BDGSparkCommand[Fasta2ADAMArgs] with Logging {
@@ -57,7 +59,13 @@ class Fasta2ADAM(protected val args: Fasta2ADAMArgs) extends BDGSparkCommand[Fas
  }
 
  log.info("Writing records to disk.")
- adamFasta.adamParquetSave(args)
+ val finalFasta = if (args.partitions > 0) {
+ adamFasta.repartition(args.partitions)
+ } else {
+ adamFasta
+ }
+
+ finalFasta.adamParquetSave(args)
  }
 }