Fix "Local variable declaration hides another field or variable" warn…

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

@@ -54,15 +54,15 @@ public static interface Options extends GCSOutputOptions, GCSOptions {}
   private static final Logger LOG = Logger.getLogger(CombineShardsFn.class.getName());
 
   final PCollectionView<Iterable<String>> shards;
-  final PCollectionView<byte[]> eofContent;
+  final PCollectionView<byte[]> eofContents;
   Aggregator<Integer, Integer> filesToCombineAggregator;
   Aggregator<Integer, Integer> combinedFilesAggregator;
   Aggregator<Integer, Integer> createdFilesAggregator;
   Aggregator<Integer, Integer> deletedFilesAggregator;
 
   public CombineShardsFn(PCollectionView<Iterable<String>> shards, PCollectionView<byte[]> eofContent) {
     this.shards = shards;
-    this.eofContent = eofContent;
+    this.eofContents = eofContent;
     filesToCombineAggregator = createAggregator("Files to combine", new SumIntegerFn());
     combinedFilesAggregator = createAggregator("Files combined", new SumIntegerFn());
     createdFilesAggregator = createAggregator("Created files", new SumIntegerFn());
@@ -76,20 +76,20 @@ public void processElement(DoFn<String, String>.ProcessContext c) throws Excepti
             c.getPipelineOptions().as(Options.class), 
             c.element(),
             c.sideInput(shards),
-            c.sideInput(eofContent));
+            c.sideInput(eofContents));
     c.output(result);
   }
 
   String combineShards(Options options, String dest,
-      Iterable<String> shards, byte[] eofContent) throws IOException {
+      Iterable<String> srcShards, byte[] eofContent) throws IOException {
     LOG.info("Combining shards into " + dest);
     final Storage.Objects storage = Transport.newStorageClient(
         options
           .as(GCSOptions.class))
           .build()
           .objects();
 
-    ArrayList<String> sortedShardsNames = Lists.newArrayList(shards);
+    ArrayList<String> sortedShardsNames = Lists.newArrayList(srcShards);
     Collections.sort(sortedShardsNames);
 
     // Write an EOF block (empty gzip block), and put it at the end.

src/main/java/htsjdk/samtools/BAMShardIndexer.java

@@ -16,15 +16,15 @@ public class BAMShardIndexer {
   private final BAMIndexBuilder indexBuilder;
 
   // Index of the reference for which the index is being written
-  int reference;
+  int referenceIndex;
 
   public BAMShardIndexer(OutputStream output, SAMFileHeader header, int reference) {
     indexBuilder = new BAMIndexBuilder(header.getSequenceDictionary(), reference);
     final boolean isFirstIndexShard = reference == 0;
     final int numReferencesToWriteInTheHeader = isFirstIndexShard ? 
         header.getSequenceDictionary().size() : 0;
     outputWriter = new BinaryBAMShardIndexWriter(numReferencesToWriteInTheHeader, output);
-    this.reference = reference;
+    this.referenceIndex = reference;
   }
 
   public void processAlignment(final SAMRecord rec) {
@@ -40,7 +40,7 @@ public void processAlignment(final SAMRecord rec) {
    * @return count of records with no coordinates.
    */
   public long finish() {
-    final BAMIndexContent content = indexBuilder.processReference(reference);
+    final BAMIndexContent content = indexBuilder.processReference(referenceIndex);
     outputWriter.writeReference(content);
     outputWriter.close();
     return indexBuilder.getNoCoordinateRecordCount();