Fixes:

- Don't know how I got the wiggle header so utterly wrong. Fixed.
 - Q-values now have a static maximum of 2000 so IGV averaging won't make everything look spikey and ugly.
 - Changing windows to size 100 for (hopefully) better resolution.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5406 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationTestRunner.java

@@ -22,9 +22,14 @@ import org.broadinstitute.sting.utils.collections.Pair;
  * To change this template use File | Settings | File Templates.
  */
 public class AssociationTestRunner {
+    final static int MAX_Q_VALUE = 2000;
     // todo -- this was written when ACs could implement interfaces, now that they extend, there's no multiple inheritance
     static Normal standardNormal = new Normal(0.0,1.0,null);
 
+    private static int pToQ(double p) {
+        return Math.min((int) Math.floor(QualityUtils.phredScaleErrorRate(p)),MAX_Q_VALUE);
+    }
+
     public static String runTests(AssociationContext context) {
         List<String> results = new ArrayList<String>();
         if ( context instanceof TStatistic) {
@@ -58,15 +63,15 @@ public class AssociationTestRunner {
      */
     public static int getQValue(AssociationContext context) {
         if ( context instanceof TStatistic ) {
-            return (int) Math.floor(QualityUtils.phredScaleErrorRate(testStudentT((TStatistic) context).second));
+            return pToQ(testStudentT((TStatistic) context).second);
         }
 
         if ( context instanceof ZStatistic ) {
-            return (int) Math.floor(QualityUtils.phredScaleErrorRate(testZ((ZStatistic) context).second));
+            return pToQ(testZ((ZStatistic) context).second);
         }
 
         if ( context instanceof UStatistic ) {
-            return (int) Math.floor(QualityUtils.phredScaleErrorRate(mannWhitneyUTest((UStatistic) context).second));
+            return pToQ(mannWhitneyUTest((UStatistic) context).second);
         }
 
         return -1;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java

@@ -135,7 +135,7 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
     public void writeWiggleHeaders(Set<AssociationContext> cons) {
         for ( AssociationContext con : cons ) {
             GenomeLoc first = getToolkit().getIntervals().iterator().next();
-            String header = String.format("fixedStep\tchrom=%s,start=%d,step=%d,span=%d",first.getContig(),first.getStart(),con.slideByValue(),con.getWindowSize());
+            String header = String.format("fixedStep chrom=%s start=%d step=%d span=%d",first.getContig(),first.getStart(),con.slideByValue(),con.getWindowSize());
             out.get(con.getClass()).printf("%s%n",header);
         }
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/BaseQualityScore.java

@@ -26,7 +26,7 @@ public class BaseQualityScore extends TStatistic {
         return (Collection) baseQuals;
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/InsertSizeDistribution.java

@@ -13,8 +13,8 @@ import java.util.List;
  * @author chartl
  */
 public class InsertSizeDistribution extends TStatistic {
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 
     public Collection<Number> map(ReadBackedPileup pileup) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MappingQuality0.java

@@ -26,8 +26,8 @@ public class MappingQuality0 extends ZStatistic {
         return new Pair<Number,Number>(mq0,total);
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateMappingQuality.java

@@ -27,7 +27,7 @@ public class MateMappingQuality extends UStatistic {
         return (Collection) mateMapQ;
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateOtherContig.java

@@ -14,8 +14,8 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  */
 public class MateOtherContig extends ZStatistic {
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 
     public Pair<Number,Number> map(ReadBackedPileup pileup) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateSameStrand.java

@@ -29,7 +29,7 @@ public class MateSameStrand extends ZStatistic {
         return new Pair<Number,Number>(mateSameStrand,numPairs);
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateUnmapped.java

@@ -29,7 +29,7 @@ public class MateUnmapped extends ZStatistic  {
         return new Pair<Number,Number>(numPairUnmapped,numMatedReads);
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ProperPairs.java

@@ -27,7 +27,7 @@ public class ProperPairs extends ZStatistic {
         return new Pair<Number,Number>(numPropPair,numReads);
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadClipping.java

@@ -33,7 +33,7 @@ public class ReadClipping extends TStatistic {
         return (Collection) clipping;
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadIndels.java

@@ -17,7 +17,7 @@ import java.util.Collection;
  * Time: 1:54 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ReadIndels extends TStatistic {
+public class ReadIndels extends UStatistic {
 
     public Collection<Number> map(ReadBackedPileup rbp) {
         ArrayList<Integer> indelElements = new ArrayList<Integer>(rbp.size());
@@ -33,7 +33,7 @@ public class ReadIndels extends TStatistic {
         return (Collection) indelElements;
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadMappingQuality.java

@@ -26,7 +26,7 @@ public class ReadMappingQuality extends TStatistic {
         return (Collection) mapQuals;
     }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/SampleDepth.java

@@ -75,8 +75,8 @@ public class SampleDepth extends UStatistic {
     // note: this is to satisfy the interface, and is never called due to override
     public Collection<Number> map(ReadBackedPileup pileup) { return null; }
 
-    public int getWindowSize() { return 200; }
+    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 25; }
+    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }