Recalibration stuff...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1810 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java

@@ -6,9 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.QualityUtils;
-
+import org.broadinstitute.sting.playground.gatk.walkers.Recalibration.LocalMapType;
-import java.util.List;
-import java.util.LinkedList;
 
 import net.sf.samtools.SAMRecord;
 
@@ -21,21 +19,24 @@ import net.sf.samtools.SAMRecord;
  */
 public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][]> {
     static final int WIN_SIDE_SIZE = 5;
-    static final int Z_SCORE_MAX = 8;
+    static final int Z_SCORE_MIN = -6;
-    static final int Z_SCORE_MULTIPLIER = 50; // bins are Z_SCORE * (this) rounded to the nearst int
+    static final int Z_SCORE_MAX = 6;
+    static final int Z_SCORE_MULTIPLIER = 20; // bins are Z_SCORE * (this) rounded to the nearst int
     static final int MM_OFFSET = 1;
     static final int MATCH_OFFSET = 0;
     static final int MAX_Q_SCORE = 2 + QualityUtils.MAX_REASONABLE_Q_SCORE;
 
     protected int WINDOW;
+    protected int Z_SCORE_RANGE;
 
     public void initialize() {
         WINDOW = 2*WIN_SIDE_SIZE+1;
+        Z_SCORE_RANGE = Z_SCORE_MAX - Z_SCORE_MIN;
     }
 
     public int[][][] reduceInit() {
-        int[][][] q = new int[Z_SCORE_MAX*Z_SCORE_MULTIPLIER+1][MAX_Q_SCORE][2];
+        int[][][] q = new int[Z_SCORE_RANGE*Z_SCORE_MULTIPLIER+1][MAX_Q_SCORE][2];
-        for ( int i = 0; i < Z_SCORE_MAX*Z_SCORE_MULTIPLIER+1; i ++ ) {
+        for ( int i = 0; i < Z_SCORE_RANGE*Z_SCORE_MULTIPLIER+1; i ++ ) {
             for ( int j = 0; j < MAX_Q_SCORE; j ++ ) {
                 for ( int k = 0; k < 2; k ++ ) {
                     q[i][j][k] = 0;
@@ -67,7 +68,7 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
 
     public void onTraversalDone( int[][][] zScoreBins ) {
         out.print( header() );
-        for ( int i = 0; i < Z_SCORE_MAX*Z_SCORE_MULTIPLIER; i ++ ) {
+        for ( int i = 0; i < Z_SCORE_RANGE*Z_SCORE_MULTIPLIER; i ++ ) {
             for ( int j = 0; j < MAX_Q_SCORE; j ++ ) {
                 out.print( formatData(zScoreBins[i][j], i, j) );
             }
@@ -84,12 +85,16 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
 
     public int calcZScoreBin( SAMRecord read, int offset ) {
         Pair<Double,Double> meanVar = calcWindowMeanVariance(read, offset);
-        double rawZ = Math.abs((getQScoreAsInt(read, offset) - meanVar.first)/Math.sqrt(meanVar.second));
+        double rawZ = (getQScoreAsInt(read, offset) - meanVar.first)/Math.sqrt(meanVar.second);
         int zBin;
-        if ( rawZ < Z_SCORE_MAX ) {
+        if ( rawZ >= Z_SCORE_MAX ) {
-            zBin = (int) Math.floor(rawZ*Z_SCORE_MULTIPLIER);
+            zBin = (int) Math.floor(Z_SCORE_RANGE*Z_SCORE_MULTIPLIER);
+        } else if ( rawZ <= Z_SCORE_MIN ) {
+            zBin = 0;
+        } else if ( rawZ > 0 ) {
+            zBin = (int) Math.floor(rawZ*Z_SCORE_MULTIPLIER) - (int) Math.floor(Z_SCORE_MIN*Z_SCORE_MULTIPLIER);
         } else {
-            zBin = Z_SCORE_MULTIPLIER*Z_SCORE_MAX;
+            zBin = (int) Math.floor(-Z_SCORE_MIN*Z_SCORE_MULTIPLIER) + (int) Math.floor(rawZ*Z_SCORE_MULTIPLIER);
         }
 
         return zBin;        
@@ -138,10 +143,6 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
     public String formatData ( int[] matchMismatch, int zScoreBin, int q ) {
         String format = "%f\t%d\t%f\t%f\t%d\t%d%n";
 
-        for ( int i = 0; i < MAX_Q_SCORE; i ++ ) {
-
-        }
-
         double zScore = ( (double) zScoreBin )/Z_SCORE_MULTIPLIER;
         int counts = matchMismatch[MATCH_OFFSET] + matchMismatch[MM_OFFSET];
         double empMMR = (((double)matchMismatch[MM_OFFSET])/counts);

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java

@@ -6,9 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.QualityUtils;
-
+import org.broadinstitute.sting.playground.gatk.walkers.Recalibration.LocalMapType;
-import java.util.List;
-import java.util.LinkedList;
 
 import net.sf.samtools.SAMRecord;
 
@@ -19,11 +17,11 @@ import net.sf.samtools.SAMRecord;
  * Time: 10:54:18 AM
  * To change this template use File | Settings | File Templates.
  */
-public class NQSCovariantByCountsWalker extends LocusWalker< LocalMapType, int[][][][] > {
+public class NQSCovariantByCountsWalker extends LocusWalker<LocalMapType, int[][][][] > {
 
     final static int SMALL_DEVIATION = 5;
     final static int LARGE_DEVIATION = 8;
-    final static int WIN_SIZE_SIDE = 4;
+    final static int WIN_SIZE_SIDE = 6;
     final static int MATCH_OFFSET = 1;
     final static int MM_OFFSET = 0;
     final static int MAX_Q_SCORE = 2 + QualityUtils.MAX_REASONABLE_Q_SCORE;

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java

@@ -5,10 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.QualityUtils;
-
+import org.broadinstitute.sting.playground.gatk.walkers.Recalibration.LocalMapType;
-import java.util.List;
-
-import net.sf.samtools.SAMRecord;
 
 
 /**

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSMismatchCovariantWalker.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
 
+import org.broadinstitute.sting.playground.gatk.walkers.Recalibration.LocalMapType;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -7,8 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.QualityUtils;
 import net.sf.samtools.SAMRecord;
 
-import java.util.List;
-
 /**
  * Created by IntelliJ IDEA.
  * User: chartl
@@ -29,7 +28,7 @@ public class NQSMismatchCovariantWalker extends LocusWalker<LocalMapType, long[]
     public static final String HEADER_FORMAT = "%s    %s     %s     %s     %s     %s%n";
 
     public long[][][] reduceInit() {
-        long[][][] mismatchesByNQS = new long[(int)QualityUtils.MAX_QUAL_SCORE+1][this.numNQSGroups()+1][2];
+        long[][][] mismatchesByNQS = new long[(int) QualityUtils.MAX_QUAL_SCORE+1][this.numNQSGroups()+1][2];
         for ( int qualityScore = 0; qualityScore <= (int) QualityUtils.MAX_QUAL_SCORE; qualityScore ++) {
             for ( int nqsGroup = 0; nqsGroup <= numNQSGroups(); nqsGroup++ ) {
                 mismatchesByNQS[qualityScore][nqsGroup][MM_OFFSET] = 0;
@@ -124,7 +123,7 @@ public class NQSMismatchCovariantWalker extends LocusWalker<LocalMapType, long[]
 
     protected boolean isDBSNP(RefMetaDataTracker tracker) {
 
-        return false; 
+        return false;
         // return ( tracker.lookup("dbSNP",null) != null );
     }
 
@@ -187,24 +186,3 @@ public class NQSMismatchCovariantWalker extends LocusWalker<LocalMapType, long[]
 
 }
 
-class LocalMapType {
-
-    public AlignmentContext context;
-    public ReferenceContext ref;
-    public RefMetaDataTracker tracker;
-
-    public LocalMapType(AlignmentContext context, ReferenceContext ref, RefMetaDataTracker tracker) {
-        this.context = context;
-        this.ref = ref;
-        this.tracker = tracker;
-    }
-
-    public int numReads() {
-        return context.numReads();
-    }
-
-    public int qScore(int read) {
-        return (int) context.getReads().get(read).getBaseQualities()[context.getOffsets().get(read)];
-    }
-
-}

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSTabularDistributionWalker.java

@@ -9,7 +9,6 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Pair;
 
 import java.util.LinkedList;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.ListIterator;
 import org.apache.log4j.Logger;