Expose sortRegions option in Spark API (#35)

Author: tdenniston

apis/spark/src/main/java/io/tiledb/libvcfnative/VCFReader.java

@@ -144,6 +144,15 @@ public VCFReader setBedFile(String uri) {
     return this;
   }
 
+  public VCFReader setSortRegions(boolean sortRegions) {
+    int rc = LibVCFNative.tiledb_vcf_reader_set_sort_regions(readerPtr, sortRegions);
+    if (rc != 0) {
+      String msg = getLastErrorMessage();
+      throw new RuntimeException("Error setting sort regions parameter: " + msg);
+    }
+    return this;
+  }
+
   public VCFReader setRangePartition(int numPartitions, int partition) {
     int rc =
         LibVCFNative.tiledb_vcf_reader_set_region_partition(readerPtr, partition, numPartitions);

apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java

@@ -49,6 +49,14 @@ public Optional<String[]> getRanges() {
     return Optional.empty();
   }
 
+  /** @return Whether or not to sort the regions */
+  public Optional<Boolean> getSortRegions() {
+    if (options.containsKey("sortRegions")) {
+      return Optional.of(Boolean.parseBoolean(options.get("sortRegions")));
+    }
+    return Optional.empty();
+  }
+
   /** @return Optional maximum memory budget (MB) */
   public Optional<Integer> getMemoryBudget() {
     if (options.containsKey("memory")) {

apis/spark/src/main/java/io/tiledb/vcf/VCFInputPartitionReader.java

@@ -234,6 +234,12 @@ private void initVCFReader() {
       vcfReader.setBedFile(bedURI.get().toString());
     }
 
+    // Set sort regions
+    Optional<Boolean> sortRegions = options.getSortRegions();
+    if (sortRegions.isPresent()) {
+      vcfReader.setSortRegions(sortRegions.get().booleanValue());
+    }
+
     // Set logical partition in array
     vcfReader.setRangePartition(
         rangePartitionInfo.getNumPartitions(), rangePartitionInfo.getIndex());