diff --git a/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java b/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
index 66de68317..c27b3c3fb 100644
--- a/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
@@ -98,7 +98,8 @@ public class BasecallingReadModel {
 
             double[] fourIntensity = new double[4];
             for (int channel = 0; channel < 4; channel++) {
-                fourIntensity[channel] = (double) ints[cycle][channel];
+                //fourIntensity[channel] = (double) ints[cycle][channel];
+                fourIntensity[channel] = (double) ints[channel][cycle];
             }
 
             basemodels[cycle].addMeanPoint(probMatrix, fourIntensity);
@@ -135,7 +136,8 @@ public class BasecallingReadModel {
 
             double[] fourIntensity = new double[4];
             for (int channel = 0; channel < 4; channel++) {
-                fourIntensity[channel] = (double) ints[cycle][channel];
+                //fourIntensity[channel] = (double) ints[cycle][channel];
+                fourIntensity[channel] = (double) ints[channel][cycle];
             }
 
             basemodels[cycle].addCovariancePoint(probMatrix, fourIntensity);
@@ -207,7 +209,8 @@ public class BasecallingReadModel {
 
             double[] fourIntensity = new double[4];
             for (int channel = 0; channel < 4; channel++) {
-                fourIntensity[channel] = (double) read.getIntensities()[cycle][channel];
+                //fourIntensity[channel] = (double) read.getIntensities()[cycle][channel];
+                fourIntensity[channel] = (double) read.getIntensities()[channel][cycle];
             }
 
             fpr.add(cycle, computeProbabilities(cycle, basePrev, qualPrev, fourIntensity));
diff --git a/java/src/org/broadinstitute/sting/secondarybase/RawRead.java b/java/src/org/broadinstitute/sting/secondarybase/RawRead.java
index 6cadd7f7d..220299537 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/RawRead.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/RawRead.java
@@ -58,7 +58,8 @@ public class RawRead implements Comparable<RawRead> {
         sequence = pastedReadString[1][4].substring(cycleBegin, cycleEnd + 1).getBytes();
 
         quals = new byte[sequence.length];
-        intensities = new short[sequence.length][4];
+        //intensities = new short[sequence.length][4];
+        intensities = new short[4][sequence.length];
 
         for (int cycle = cycleBegin, offset = 0; cycle <= cycleEnd; cycle++, offset++) {
             byte maxQual = -50;
@@ -75,7 +76,8 @@ public class RawRead implements Comparable<RawRead> {
                 double doubleChannelIntensity = Double.valueOf(pastedReadString[0][fullReadIndex]);
                 short shortChannelIntensity = (short) doubleChannelIntensity;
 
-                intensities[offset][channel] = shortChannelIntensity;
+                //intensities[offset][channel] = shortChannelIntensity;
+                intensities[channel][offset] = shortChannelIntensity;
             }
         }
     }
@@ -181,14 +183,14 @@ public class RawRead implements Comparable<RawRead> {
     /**
      * Get the raw read intensities.
      *
-     * @return the (readLength)x(numChannels) array of raw intensities
+     * @return the (numChannels)x(readLength) array of raw intensities
      */
     public short[][] getIntensities() { return intensities; }
 
     /**
      * Set the raw intensities.
      *
-     * @param intensities  the (readLength)x(numChannels) array of raw intensities
+     * @param intensities  the (numChannels)x(readLength) array of raw intensities
      */
     public void setIntensities(short[][] intensities) { this.intensities = intensities; }
 
@@ -239,12 +241,17 @@ public class RawRead implements Comparable<RawRead> {
 
         byte[] newSequence = new byte[cycleStop - cycleStart + 1];
         byte[] newQuals = new byte[cycleStop - cycleStart + 1];
-        short[][] newIntensities = new short[cycleStop - cycleStart + 1][4];
+        //short[][] newIntensities = new short[cycleStop - cycleStart + 1][4];
+        short[][] newIntensities = new short[4][cycleStop - cycleStart + 1];
 
         for (int cycle = cycleStart, offset = 0; cycle <= cycleStop; cycle++, offset++) {
             newSequence[offset] = sequence[cycle];
             newQuals[offset] = quals[cycle];
-            newIntensities[offset] = intensities[cycle];
+            //newIntensities[offset] = intensities[cycle];
+
+            for (int channel = 0; channel < 4; channel++) {
+                newIntensities[channel][offset] = intensities[channel][cycle];
+            }
         }
 
         subRead.setSequence(newSequence);