diff --git a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
index 97a81e99f..d2fae4143 100644
--- a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
@@ -27,27 +27,18 @@ public class FirecrestFileParser extends AbstractFirecrestFileParser {
     private BasicTextFileParser parser;
     private final FormatUtil formatter = new FormatUtil();
     private final File[] intensityFiles;
-    private int cycle_start = -1;
-    private int cycle_stop = -1;
 
     /**
      * Constructor
      *
      * @param firecrestDirectory  directory where the Firecrest files can be located
-     * @param lane              the lane to parse
+     * @param lane                the lane to parse
      */
     public FirecrestFileParser(final File firecrestDirectory, final int lane) {
         super(firecrestDirectory, lane);
         intensityFiles = getFilesMatchingRegexp("s_" + lane + "_\\d{4}_int.txt(.gz)?");
     }
 
-    public FirecrestFileParser(final File firecrestDirectory, final int lane, final int cycle_start, final int cycle_stop) {
-        super(firecrestDirectory, lane);
-        intensityFiles = getFilesMatchingRegexp("s_" + lane + "_\\d{4}_int.txt(.gz)?");
-        this.cycle_start = cycle_start;
-        this.cycle_stop = cycle_stop;
-    }
-
     @Override
     public boolean isValidFirecrestDirectory() {
         return (intensityFiles.length > 0);
@@ -56,7 +47,6 @@ public class FirecrestFileParser extends AbstractFirecrestFileParser {
     /**
      * Sorts the relevant files in the firecrestDirectory.  Does some basic sanity checking to ensure that some files
      * are found and that they are the expected multiple for paired-end or not.
-     *
      */
     @Override
     protected void prepareToIterate() {
@@ -88,24 +78,16 @@ public class FirecrestFileParser extends AbstractFirecrestFileParser {
 
         int intensityOffset = 4;
         int numIntensities = (data.length - 4)/4;
-        FourIntensity[] intensities = new FourIntensity[numIntensities];
+
+        double[][] intensities = new double[numIntensities][4];
 
         for (int cycle = 0, index = intensityOffset; cycle < numIntensities; cycle++) {
-            float[] fIntensities = new float[4];
             for (int channel = 0; channel < 4; channel++, index++) {
-                fIntensities[channel] = formatter.parseFloat(data[index]);
+                intensities[cycle][channel] = formatter.parseFloat(data[index]);
             }
-
-            intensities[cycle] = new FourIntensity(fIntensities);
         }
 
-        FourIntensity[] intensities2 = new FourIntensity[(cycle_start > 0 && cycle_stop > 0 && cycle_stop > cycle_start) ? (cycle_stop - cycle_start) : numIntensities];
-
-        for (int cycle = 0, offset = (cycle_start >= 0 ? cycle_start : 0); cycle < intensities2.length; cycle++) {
-            intensities2[cycle] = intensities[offset + cycle];
-        }
-
-        return new FirecrestReadData(lane, tile, x, y, intensities2);
+        return new FirecrestReadData(lane, tile, x, y, intensities);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
index bd8abc979..feb997dc6 100644
--- a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
@@ -19,7 +19,7 @@ public class FirecrestReadData {
     final private int tileNumber;
     final private int xCoordinate;
     final private int yCoordinate;
-    final private FourIntensity[] intensities;
+    final private double[][] intensities;
 
 
     /**
@@ -31,7 +31,7 @@ public class FirecrestReadData {
      * @param yCoordinate
      * @param intensities
      */
-    public FirecrestReadData(int laneNumber, int tileNumber, int xCoordinate, int yCoordinate, FourIntensity[] intensities) {
+    public FirecrestReadData(int laneNumber, int tileNumber, int xCoordinate, int yCoordinate, double[][] intensities) {
         this.laneNumber = laneNumber;
         this.tileNumber = tileNumber;
         this.xCoordinate = xCoordinate;
@@ -52,6 +52,6 @@ public class FirecrestReadData {
     public int getTileNumber() { return tileNumber; }
     public int getXCoordinate() { return xCoordinate; }
     public int getYCoordinate() { return yCoordinate; }
-    public FourIntensity[] getIntensities() { return intensities; }
+    public double[][] getIntensities() { return intensities; }
 
 }