Add missing loadVariantContexts(String, ValidationStringency) method.

bigdatagenomics · Aug 27, 2019 · daf9be6 · daf9be6
1 parent 9518eef
commit daf9be6
Showing 1 changed file with 19 additions and 0 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -2838,6 +2838,25 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     if (regions.nonEmpty) genotypesDatasetBound.filterByOverlappingRegions(regions) else genotypesDatasetBound
   }
 
+  /**
+   * Load a path name in VCF or Parquet format into a VariantContextDataset.
+   *
+   * @param pathName The path name to load variant context records from.
+   *   Globs/directories are supported.
+   * @param stringency The validation stringency to use when validating VCF format.
+   * @return Returns a VariantContextDataset.
+   */
+  def loadVariantContexts(
+    pathName: String,
+    stringency: ValidationStringency): VariantContextDataset = {
+
+    if (isVcfExt(pathName)) {
+      loadVcf(pathName, stringency)
+    } else {
+      loadParquetVariantContexts(pathName)
+    }
+  }
+
   /**
    * Load a path name in VCF or Parquet format into a VariantContextDataset.
    *