Merge pull request #652 from erictu/master

added filterByOverlappingRegion in GeneFeatureRDDFunctions
bigdatagenomics · Apr 17, 2015 · 1b79e25 · 1b79e25
2 parents 3be1fb0 + 1a5178e
commit 1b79e25
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/GeneFeatureRDDFunctions.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/GeneFeatureRDDFunctions.scala
@@ -122,5 +122,13 @@ class GeneFeatureRDDFunctions(featureRDD: RDD[Feature]) extends Serializable wit
 
     genes
   }
+
+  def filterByOverlappingRegion(query: ReferenceRegion): RDD[Feature] = {
+    def overlapsQuery(rec: Feature): Boolean =
+      rec.getContig.getContigName.toString == query.referenceName &&
+        rec.getStart < query.end &&
+        rec.getEnd > query.start
+    featureRDD.filter(overlapsQuery)
+  }
 }