Add command line option re: creating references from FASTA sources.

bigdatagenomics · Jun 12, 2019 · 81ed51f · 81ed51f
1 parent 450f8c6
commit 81ed51f
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSequences.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSequences.scala
@@ -41,6 +41,10 @@ class TransformSequencesArgs extends Args4jBase with ParquetSaveArgs {
     usage = "Location to write ADAM sequence data. If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
+  @Args4jOption(required = false, name = "-create_reference",
+    usage = "Create reference from sequence names and lengths. Defaults to false.")
+  var createReference: Boolean = false
+
   @Args4jOption(required = false, name = "-single",
     usage = "Save as a single file, for the text formats.")
   var single: Boolean = false
@@ -66,6 +70,7 @@ class TransformSequences(val args: TransformSequencesArgs)
       case Alphabet.PROTEIN => sc.loadProteinSequences(args.sequencesFile, optPredicate = None, optProjection = None)
       case Alphabet.RNA     => sc.loadRnaSequences(args.sequencesFile, optPredicate = None, optProjection = None)
     }
-    sequences.save(args.outputPath, args.single, args.disableFastConcat)
+    val maybeCreateReference = if (args.createReference) sequences.createSequenceDictionary() else sequences
+    maybeCreateReference.save(args.outputPath, args.single, args.disableFastConcat)
   }
 }
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSlices.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSlices.scala
@@ -44,6 +44,10 @@ class TransformSlicesArgs extends Args4jBase with ParquetSaveArgs {
     usage = "Maximum slice length. Defaults to 10000L.")
   var maximumLength: Long = 10000L
 
+  @Args4jOption(required = false, name = "-create_reference",
+    usage = "Create reference from sequence names and lengths. Defaults to false.")
+  var createReference: Boolean = false
+
   @Args4jOption(required = false, name = "-single",
     usage = "Save as a single file, for the text formats.")
   var single: Boolean = false
@@ -59,11 +63,13 @@ class TransformSlices(val args: TransformSlicesArgs)
   val companion = TransformSlices
 
   def run(sc: SparkContext) {
-    sc.loadSlices(
+    val slices = sc.loadSlices(
       args.slicesFile,
       maximumLength = args.maximumLength,
       optPredicate = None,
       optProjection = None
-    ).save(args.outputPath, args.single, args.disableFastConcat)
+    )
+    val maybeCreateReference = if (args.createReference) slices.createSequenceDictionary() else slices
+    maybeCreateReference.save(args.outputPath, args.single, args.disableFastConcat)
   }
 }