diff --git a/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java b/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java
index 753d955..1ed0390 100644
--- a/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java
+++ b/src/main/java/com/google/cloud/genomics/dataflow/functions/CombineShardsFn.java
@@ -54,7 +54,7 @@ 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;
@@ -62,7 +62,7 @@ public static interface Options extends GCSOutputOptions, GCSOptions {}
   
   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());
@@ -76,12 +76,12 @@ 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
@@ -89,7 +89,7 @@ String combineShards(Options options, String dest,
           .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.
diff --git a/src/main/java/htsjdk/samtools/BAMShardIndexer.java b/src/main/java/htsjdk/samtools/BAMShardIndexer.java
index 6821c6c..3ded45c 100644
--- a/src/main/java/htsjdk/samtools/BAMShardIndexer.java
+++ b/src/main/java/htsjdk/samtools/BAMShardIndexer.java
@@ -16,7 +16,7 @@ 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);
@@ -24,7 +24,7 @@ public BAMShardIndexer(OutputStream output, SAMFileHeader header, int reference)
     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();