diff --git a/src/main/java/org/broad/igv/ucsc/bb/BBDataSource.java b/src/main/java/org/broad/igv/ucsc/bb/BBDataSource.java
index 74c8c165b4..0016d3f351 100644
--- a/src/main/java/org/broad/igv/ucsc/bb/BBDataSource.java
+++ b/src/main/java/org/broad/igv/ucsc/bb/BBDataSource.java
@@ -131,8 +131,6 @@ private void initMinMax() {
 //            dataMax = 100;
 //        }
 //    }
-
-
     public double getDataMax() {
         return dataMax;
     }
@@ -197,7 +195,7 @@ protected List<LocusScore> getPrecomputedSummaryScores(String chr, int start, in
 
 
             Chromosome chromosome = genome.getChromosome(chr);
-            if(chromosome == null) {
+            if (chromosome == null) {
                 throw new RuntimeException("Unexpected chromosome name: " + chr);
             }
 
@@ -210,11 +208,11 @@ protected List<LocusScore> getPrecomputedSummaryScores(String chr, int start, in
                 return null;
             } else {
                 long rTreeOffset = zlHeader.indexOffset;
+                int chrIdx = reader.getIdForChr(chr);
                 List<byte[]> chunks = this.reader.getLeafChunks(chr, start, chr, end, rTreeOffset);
-
                 List<LocusScore> features = new ArrayList<>();
                 for (byte[] c : chunks) {
-                    reader.decodeZoomData(c, windowFunction, features);
+                    reader.decodeZoomData(c, chrIdx, start, end, windowFunction, features);
                 }
                 return features;
             }
@@ -272,7 +270,7 @@ private List<LocusScore> getWholeGenomeScores() {
 
                     List<LocusScore> features = new ArrayList<>();
                     for (byte[] c : chunks) {
-                        reader.decodeZoomData(c, windowFunction, features);
+                        reader.decodeZoomData(c, -1, -1, -1, windowFunction, features);
                     }
 
                     for (LocusScore s : features) {
diff --git a/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java b/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java
index 0ff3ad588a..38a46bcfd7 100644
--- a/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java
+++ b/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java
@@ -95,10 +95,11 @@ public void close() {
     public Iterator<BasicFeature> getFeatures(String chr, int start, int end) throws IOException {
 
         long rTreeOffset = reader.header.fullIndexOffset;
+        int chrIdx = reader.getIdForChr(chr);
         List<byte[]> chunks = this.reader.getLeafChunks(chr, start, chr, end, rTreeOffset);
         List features = new ArrayList<>();
         for (byte[] c : chunks) {
-            features.addAll(reader.decodeFeatures(c));
+            features.addAll(reader.decodeFeatures(c, chrIdx, start, end));
         }
         return new FeatureIterator(features, start, end);
     }
diff --git a/src/main/java/org/broad/igv/ucsc/bb/BBFile.java b/src/main/java/org/broad/igv/ucsc/bb/BBFile.java
index 32e2dda292..b573c81d6f 100644
--- a/src/main/java/org/broad/igv/ucsc/bb/BBFile.java
+++ b/src/main/java/org/broad/igv/ucsc/bb/BBFile.java
@@ -411,7 +411,7 @@ public BasicFeature search(String term) throws IOException {
                 byte[] buffer = new byte[size];
                 is.seek(start);
                 is.readFully(buffer);
-                List<BasicFeature> features = decodeFeatures(buffer);
+                List<BasicFeature> features = decodeFeatures(buffer, -1, -1, -1);
                 BasicFeature largest = features.stream().reduce((f1, f2) -> {
                     int l1 = f1.getEnd() - f1.getStart();
                     int l2 = f2.getEnd() - f2.getStart();
@@ -423,7 +423,7 @@ public BasicFeature search(String term) throws IOException {
         return null;
     }
 
-    List<BasicFeature> decodeFeatures(byte[] buffer) {
+    List<BasicFeature> decodeFeatures(byte[] buffer, int chrIdx, int start, int end) {
         List<BasicFeature> features = new ArrayList<>();
         byte[] uncompressed;
         if (this.header.uncompressBuffSize > 0) {
@@ -440,8 +440,13 @@ List<BasicFeature> decodeFeatures(byte[] buffer) {
             int chromStart = bb.getInt();
             int chromEnd = bb.getInt();
             String restOfFields = bb.getString();
-            String chr = getChrForId(chromId);
 
+            if (chrIdx > 0) {
+                if (chromId < chrIdx || (chromId == chrIdx && chromEnd < start)) continue;
+                else if (chromId > chrIdx || (chromId == chrIdx && chromStart >= end)) break;
+            }
+
+            String chr = getChrForId(chromId);
             final BedData bedData = new BedData(chr, chromStart, chromEnd, restOfFields);
             final BasicFeature feature = bedCodec.decode(bedData);
             features.add(feature);
@@ -449,7 +454,7 @@ List<BasicFeature> decodeFeatures(byte[] buffer) {
         return features;
     }
 
-    List<LocusScore> decodeZoomData(byte[] buffer, WindowFunction windowFunction, List<LocusScore> features) {
+    List<LocusScore> decodeZoomData(byte[] buffer, int chrIdx, int start, int end, WindowFunction windowFunction, List<LocusScore> features) {
 
         byte[] uncompressed;
         if (header.uncompressBuffSize > 0) {
@@ -470,6 +475,11 @@ List<LocusScore> decodeZoomData(byte[] buffer, WindowFunction windowFunction, Li
             float sumData = bb.getFloat();
             float sumSquares = bb.getFloat();
 
+            if (chrIdx > 0) {
+                if (chromId < chrIdx || (chromId == chrIdx && chromEnd < start)) continue;
+                else if (chromId > chrIdx || (chromId == chrIdx && chromStart >= end)) break;
+            }
+
             String chr = getChrForId(chromId);
 
             float value;