GenomicRDD.scala - removed commented out code

bigdatagenomics · Mar 9, 2018 · aee7c32 · aee7c32
1 parent a6f2f68
commit aee7c32
Showing 1 changed file with 4 additions and 22 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
@@ -2212,39 +2212,21 @@ trait DatasetBoundGenomicDataset[T, U <: Product, V <: GenomicDataset[T, U, V]]
 
   private def referenceRegionsToDatasetQueryString(regions: Iterable[ReferenceRegion]): String = {
 
-    val old = if (Try(dataset("positionBin")).isSuccess) {
-      regions.map(r => "(contigName=" + "\'" + r.referenceName +
-        "\' and positionBin >= \'" + ((scala.math.floor(r.start / optPartitionBinSize.get).toInt).toInt - optLookbackPartitions.get) +
-        "\' and positionBin < \'" + (scala.math.floor(r.end / optPartitionBinSize.get).toInt + 1) +
-        "\' and (end > " + r.start + " and start < " + r.end + "))")
-        .mkString(" or ")
-    } else { // if no positionBin field is found then construct query without bin optimization
-      regions.map(r => "(contigName=" + "\'" + r.referenceName +
-        "\' and (end > " + r.start + " and start < " + r.end + "))")
-        .mkString(" or ")
-    }
-    println("this was the old queyr stirng: " + old)
-
-    //test if this dataset is bound to Partitioned Parquet having field positionBin
-    val x = if (Try(dataset("positionBin")).isSuccess) {
+    if (Try(dataset("positionBin")).isSuccess) {
       regions.map(r =>
-        s"(contigName=\'${r.referenceName}\' and positionBin >= " +
+          s"(contigName=\'${r.referenceName}\' and positionBin >= " +
           s"\'${(scala.math.floor(r.start / optPartitionBinSize.get).toInt) - optLookbackPartitions.get}\'" +
           s" and positionBin < \'${(scala.math.floor(r.end / optPartitionBinSize.get).toInt + 1)}\'" +
           s" and (end > ${r.start} and start < ${r.end}))"
       ).mkString(" or ")
     } else { // if no positionBin field is found then construct query without bin optimization
       regions.map(r =>
-        s"(contigName=\'${r.referenceName} \' " +
+          s"(contigName=\'${r.referenceName} \' " +
           s"and (end > ${r.start} and end < ${r.end}))")
         .mkString(" or ")
     }
-
-    println("This is the query String: " + x)
-    x
-
   }
-
+  
   override def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): V = {
     if (isPartitioned) {
       transformDataset((d: Dataset[U]) =>