diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
index ec917bbd..a498831b 100644
--- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
+++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
@@ -16,20 +16,18 @@
 
 public class VariantStore implements Serializable {
 	private static final long serialVersionUID = -6970128712587609414L;
+	public static final String VARIANT_STORE_JAVABIN_FILENAME = "variantStore.javabin";
+	public static final String VARIANT_SPEC_INDEX_JAVABIN_FILENAME = "variantSpecIndex.javabin";
 	private static Logger log = LoggerFactory.getLogger(VariantStore.class);
 	public static final int BUCKET_SIZE = 1000;
 
-	public static final String VARIANT_SPEC_INDEX_FILE = "variantSpecIndex.javabin";
+	public static final String VARIANT_SPEC_INDEX_FILE = VARIANT_SPEC_INDEX_JAVABIN_FILENAME;
 
 	private BigInteger emptyBitmask;
 	private String[] patientIds;
 
 	private transient String[] variantSpecIndex;
-
-	private Integer variantStorageSize;
-
-	private String[] vcfHeaders = new String[24];
-
+	
 	private Map<String, FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>>> variantMaskStorage = new TreeMap<>();
 
 	public Map<String, FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>>> getVariantMaskStorage() {
@@ -48,7 +46,7 @@ public void setVariantSpecIndex(String[] variantSpecIndex) {
 	}
 
 	public static VariantStore readInstance(String genomicDataDirectory) throws IOException, ClassNotFoundException {
-		ObjectInputStream ois = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + "variantStore.javabin")));
+		ObjectInputStream ois = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + VARIANT_STORE_JAVABIN_FILENAME)));
 		VariantStore variantStore = (VariantStore) ois.readObject();
 		ois.close();
 		variantStore.getVariantMaskStorage().values().forEach(store -> {
@@ -60,14 +58,14 @@ public static VariantStore readInstance(String genomicDataDirectory) throws IOEx
 	}
 
 	public void writeInstance(String genomicDirectory) {
-		try (FileOutputStream fos = new FileOutputStream(new File(genomicDirectory, "variantStore.javabin"));
+		try (FileOutputStream fos = new FileOutputStream(new File(genomicDirectory, VARIANT_STORE_JAVABIN_FILENAME));
 			 GZIPOutputStream gzos = new GZIPOutputStream(fos);
 			 ObjectOutputStream oos = new ObjectOutputStream(gzos);) {
 			oos.writeObject(this);
 		} catch (IOException e) {
 			throw new UncheckedIOException(e);
 		}
-		try (FileOutputStream fos = new FileOutputStream(new File(genomicDirectory, "variantSpecIndex.javabin"));
+		try (FileOutputStream fos = new FileOutputStream(new File(genomicDirectory, VARIANT_SPEC_INDEX_JAVABIN_FILENAME));
 			 GZIPOutputStream gzos = new GZIPOutputStream(fos);
 			 ObjectOutputStream oos = new ObjectOutputStream(gzos);) {
 			oos.writeObject(Arrays.asList(variantSpecIndex));
@@ -76,41 +74,6 @@ public void writeInstance(String genomicDirectory) {
 		}
 	}
 
-	public Map<String, int[]> countVariants() {
-		HashMap<String, Integer> countOffsetMap = new HashMap<String, Integer>();
-		TreeMap<String, int[]> counts = new TreeMap<>();
-		for (String contig : variantMaskStorage.keySet()) {
-			counts.put(contig, new int[5]);
-			FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>> storage = variantMaskStorage
-					.get(contig);
-			storage.keys().stream().forEach((Integer key) -> {
-				int[] contigCounts = counts.get(contig);
-				Collection<VariableVariantMasks> values = storage.get(key).values();
-				contigCounts[0] += values.stream().collect(Collectors.summingInt((VariableVariantMasks masks) -> {
-					return masks.heterozygousMask != null ? 1 : 0;
-				}));
-				contigCounts[1] += values.stream().collect(Collectors.summingInt((VariableVariantMasks masks) -> {
-					return masks.homozygousMask != null ? 1 : 0;
-				}));
-				contigCounts[2] += values.stream().collect(Collectors.summingInt((VariableVariantMasks masks) -> {
-					return masks.heterozygousNoCallMask != null ? 1 : 0;
-				}));
-				contigCounts[3] += values.stream().collect(Collectors.summingInt((VariableVariantMasks masks) -> {
-					return masks.homozygousNoCallMask != null ? 1 : 0;
-				}));
-				contigCounts[4] += values.stream().collect(Collectors.summingInt((VariableVariantMasks masks) -> {
-					return masks.heterozygousMask != null || masks.homozygousMask != null
-							|| masks.heterozygousNoCallMask != null || masks.homozygousNoCallMask != null ? 1 : 0;
-				}));
-			});
-		}
-		return counts;
-	}
-
-	public String[] getVCFHeaders() {
-		return vcfHeaders;
-	}
-
 	public String[] getPatientIds() {
 		return patientIds;
 	}
@@ -124,11 +87,6 @@ public Optional<VariableVariantMasks> getMasks(String variant, VariantBucketHold
 		int chrOffset = Integer.parseInt(segments[1]) / BUCKET_SIZE;
 		String contig = segments[0];
 
-//		if (Level.DEBUG.equals(log.getEffectiveLevel())) {
-//			log.debug("Getting masks for variant " + variant + "  Same bucket test: " + (bucketCache.lastValue != null
-//					&& contig.contentEquals(bucketCache.lastContig) && chrOffset == bucketCache.lastChunkOffset));
-//		}
-
 		if (bucketCache.lastValue != null && contig.contentEquals(bucketCache.lastContig)
 				&& chrOffset == bucketCache.lastChunkOffset) {
 			// TODO : This is a temporary efficiency hack, NOT THREADSAFE!!!
@@ -166,10 +124,6 @@ public List<VariableVariantMasks> getMasksForDbSnpSpec(String variant) {
 		}
 	}
 
-	public String[] getHeaders() {
-		return vcfHeaders;
-	}
-
 	public void open() {
 		variantMaskStorage.values().stream().forEach((fbbis -> {
 			if (fbbis != null) {
@@ -190,34 +144,6 @@ public void setPatientIds(String[] patientIds) {
 		this.patientIds = patientIds;
 	}
 
-	public int getVariantStorageSize() {
-		return variantStorageSize;
-	}
-
-	public void setVariantStorageSize(int variantStorageSize) {
-		this.variantStorageSize = variantStorageSize;
-	}
-
-	public List<VariantMasks> getMasksForRangesOfChromosome(String contigForGene, List<Integer> offsetsForGene,
-			RangeSet<Integer> rangeSetsForGene) throws IOException {
-		FileBackedJsonIndexStorage masksForChromosome = variantMaskStorage.get(contigForGene);
-		Set<Integer> bucketsForGene = offsetsForGene.stream().map((offset) -> {
-			return offset / BUCKET_SIZE;
-		}).collect(Collectors.toSet());
-		List<VariantMasks> masks = new ArrayList<VariantMasks>();
-		for (Integer bucket : bucketsForGene) {
-			Map<String, VariantMasks> variantMaskBucket = (Map<String, VariantMasks>) masksForChromosome.get(bucket);
-			variantMaskBucket.keySet().stream().filter((String spec) -> {
-				int offsetForVariant = Integer.parseInt(spec.split(",")[1]);
-				return rangeSetsForGene.contains(offsetForVariant);
-			}).forEach((spec) -> {
-				System.out.println(spec);
-				masks.add(variantMaskBucket.get(spec));
-			});
-		}
-		return masks;
-	}
-
 	public BigInteger emptyBitmask() {
 		if (emptyBitmask == null || emptyBitmask.testBit(emptyBitmask.bitLength() / 2)) {
 			String emptyVariantMask = "";
@@ -229,19 +155,16 @@ public BigInteger emptyBitmask() {
 		return emptyBitmask;
 	}
 
+	@SuppressWarnings("unchecked")
 	public static String[] loadVariantIndexFromFile(String genomicDataDirectory) {
 		try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + "/" + VARIANT_SPEC_INDEX_FILE)));){
 
 			List<String> variants = (List<String>) objectInputStream.readObject();
 			return variants.toArray(new String[0]);
 
-		} catch (FileNotFoundException e) {
-			throw new RuntimeException(e);
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		} catch (ClassNotFoundException e) {
+		} catch (IOException | ClassNotFoundException e) {
 			throw new RuntimeException(e);
 		}
-	}
+    }
 
 }