a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java

@@ -108,7 +108,7 @@ public class GLFReader implements Iterator<GLFRecord> {
         short rmsMapping = inputBinaryCodec.readUByte();
         double[] lkValues = new double[LikelihoodObject.GENOTYPE.values().length];
         for (int x = 0; x < LikelihoodObject.GENOTYPE.values().length; x++) {
-            lkValues[x] = (inputBinaryCodec.readUByte() / GLFRecord.LIKELIHOOD_SCALE_FACTOR + min_lk);
+            lkValues[x] = ((double)inputBinaryCodec.readUByte() / GLFRecord.LIKELIHOOD_SCALE_FACTOR + (double)min_lk);
         }
         return new GLFSingleCall(referenceName, refBase, (int)(offset+currentLocation), readDepth, rmsMapping, lkValues);
     }

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java

@@ -172,13 +172,12 @@ public abstract class GLFRecord {
      *
      * @param chromosome        the reference contig, as a String
      * @param base              the reference base in the reference, as a REF_BASE
-     * @param offset            the offset from the last call
      * @param position          the distance from the beginning of the reference seq
      * @param minimumLikelihood it's minimum likelihood
      * @param readDepth         the read depth at this position
      * @param rmsMapQ           the root mean square of the mapping quality
      */
-    private void validateInput(String chromosome, REF_BASE base, long position, short minimumLikelihood, int readDepth, short rmsMapQ) {
+    private void validateInput(String chromosome, REF_BASE base, long position, double minimumLikelihood, int readDepth, short rmsMapQ) {
         // add any validation to the contig string here
         this.contig = chromosome;
 
@@ -189,11 +188,10 @@ public abstract class GLFRecord {
         }
         this.position = position;
 
-
         if (minimumLikelihood > 255 || minimumLikelihood < 0) {
             throw new IllegalArgumentException("minimumLikelihood is out of bounds (0 to 0xffffffff) value passed = " + minimumLikelihood);
         }
-        this.minimumLikelihood = minimumLikelihood;
+        this.minimumLikelihood = GLFRecord.toCappedShort(minimumLikelihood);
 
         if (readDepth > 16777215 || readDepth < 0) {
             throw new IllegalArgumentException("readDepth is out of bounds (0 to 0xffffff) value passed = " + readDepth);
@@ -259,14 +257,14 @@ public abstract class GLFRecord {
      *
      * @return
      */
-    protected static short findMin(double vals[]) {
+    protected static double findMin(double vals[]) {
         if (vals.length < 1) throw new StingException("findMin: an array of size < 1 was passed in");
 
         double min = vals[0];
         for (double d : vals)
             if (d < min) min = d;
 
-        return GLFRecord.toCappedShort(min);
+        return min;
     }
 
     public REF_BASE getRefBase() {

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFSingleCall.java

@@ -37,7 +37,7 @@ import net.sf.samtools.util.BinaryCodec;
  */
 public class GLFSingleCall extends GLFRecord {
 
-    // our likelihoods object
+    // our likelihoods array
     private double likelihoods[];
 
     /**
@@ -64,9 +64,12 @@ public class GLFSingleCall extends GLFRecord {
     void write(BinaryCodec out, GLFRecord lastRec) {
         super.write(out, lastRec);
         short[] adjusted = new short[likelihoods.length];
+        // find the minimum likelihood as a double
+        double minLikelihood = GLFRecord.findMin(likelihoods);
+        
         // we want to scale our values
         for (int x = 0; x < likelihoods.length; x++) {
-            adjusted[x] = GLFRecord.toCappedShort(LIKELIHOOD_SCALE_FACTOR * (Math.round(likelihoods[x]) - this.minimumLikelihood));
+            adjusted[x] = GLFRecord.toCappedShort(Math.round(LIKELIHOOD_SCALE_FACTOR * (likelihoods[x] - minLikelihood)));
         }
         try {
             for (short value : adjusted) {

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -129,7 +129,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testOtherFormat() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "GLF", "cc1782d734e0a02fef00900a6db0e550" );
+        e.put( "GLF", "d5d1c5ea8d42712d5509cd1c9c38359d" );
         e.put( "GELI_BINARY", "764a0fed1b3cf089230fd91f3be9c2df" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {