Minor optimization to skip cloning of non-variant segments.

pom.xml

@@ -314,6 +314,18 @@
           </execution>
         </executions>
       </plugin>
+
+      <!--
+      Use a newer version of the plugin to avoid long build times on
+      machines with slow Unix group lookups
+      https://www.mail-archive.com/issues@maven.apache.org/msg95302.html
+      -->
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>2.6</version>
+      </plugin>
+
     </plugins>
   </build>
 

src/main/java/com/google/cloud/genomics/dataflow/functions/JoinNonVariantSegmentsWithVariants.java

@@ -183,8 +183,8 @@ public void processElement(ProcessContext context) {
       List<Variant> blockRecords = new LinkedList<>();
 
       for (Variant record : records) {
-        Variant updatedRecord = record.clone();
-        if (!VariantUtils.IS_NON_VARIANT_SEGMENT.apply(updatedRecord)) {
+        if (!VariantUtils.IS_NON_VARIANT_SEGMENT.apply(record)) {
+          Variant updatedRecord = record.clone();
           // TODO: determine and implement the correct criteria for overlaps of non-SNP variants
           if (VariantUtils.IS_SNP.apply(updatedRecord)) {
             for (Iterator<Variant> iterator = blockRecords.iterator(); iterator.hasNext();) {
@@ -200,7 +200,7 @@ public void processElement(ProcessContext context) {
           }
           context.output(updatedRecord);
         } else {
-          blockRecords.add(updatedRecord);
+          blockRecords.add(record);
         }
       }
     }