Switch from togglable wiggle output to togglable bedgraph format. Can be pulled directly into IGV to show the statistics values. I'll need to bug jim to allow value-toggling in a bedgraph, currently 2nd and 3rd columns are just ignored.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5492 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -22,7 +22,7 @@ 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;
+    final static int MAX_Q_VALUE = Integer.MAX_VALUE;
     // 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);
 
@@ -30,6 +30,25 @@ public class AssociationTestRunner {
         return Math.min((int) Math.floor(QualityUtils.phredScaleErrorRate(p)),MAX_Q_VALUE);
     }
 
+    public static Pair<Double,Pair<Double,Integer>> getTestValues(AssociationContext context) {
+        if ( context instanceof TStatistic) {
+            Pair<Double,Double> t = testStudentT((TStatistic) context);
+            return new Pair<Double,Pair<Double,Integer>> (t.first,new Pair<Double,Integer>(t.second,pToQ(t.second)));
+        }
+
+        if ( context instanceof ZStatistic) {
+            Pair<Double,Double> z = testZ((ZStatistic) context);
+            return new Pair<Double,Pair<Double,Integer>> (z.first,new Pair<Double,Integer>(z.second,pToQ(z.second)));
+        }
+
+        if ( context instanceof UStatistic ) {
+            Pair<Double,Double> u = mannWhitneyUTest((UStatistic) context);
+            return new Pair<Double,Pair<Double,Integer>> ( u.first, new Pair<Double,Integer>(u.second,pToQ(u.second)));
+        }
+
+        return null;
+    }
+
     public static String runTests(AssociationContext context) {
         List<String> results = new ArrayList<String>();
         if ( context instanceof TStatistic) {
@@ -56,32 +75,12 @@ public class AssociationTestRunner {
         return buf.toString();
     }
 
-    /**
-     * Just gets the Q value associated with a particular association context.
-     * @param context
-     * @return
-     */
-    public static int getQValue(AssociationContext context) {
-        if ( context instanceof TStatistic ) {
-            return pToQ(testStudentT((TStatistic) context).second);
-        }
-
-        if ( context instanceof ZStatistic ) {
-            return pToQ(testZ((ZStatistic) context).second);
-        }
-
-        if ( context instanceof UStatistic ) {
-            return pToQ(mannWhitneyUTest((UStatistic) context).second);
-        }
-
-        return -1;
-    }
 
     public static String runStudentT(TStatistic context) {
         Pair<Double,Double> stats = testStudentT(context);
         double t = stats.first;
         double p = stats.second;
-        return String.format("T: %.2f\tP: %.2e\tQ: %d",t,p,(int)Math.floor(QualityUtils.phredScaleErrorRate(p)));
+        return String.format("T: %.2f\tP: %.2e\tQ: %d",t,p,pToQ(p));
     }
 
     public static Pair<Double,Double> testStudentT(TStatistic context) {
@@ -110,7 +109,7 @@ public class AssociationTestRunner {
         Pair<Double,Double> stats = testZ(context);
         double z = stats.first;
         double p = stats.second;
-        return String.format("Z: %.2f\tP: %.2e\tQ: %d",z,p,(int)Math.floor(QualityUtils.phredScaleErrorRate(p)));
+        return String.format("Z: %.2f\tP: %.2e\tQ: %d",z,p,pToQ(p));
     }
 
     public static Pair<Double,Double> testZ(ZStatistic context) {
@@ -137,7 +136,7 @@ public class AssociationTestRunner {
         // note: u statistic (U) is relatively useless for recalibrating outside of the context of m and n
         // thus we report V = (U - (m*n+1)/2)/(n*m*(n+m+1)/12)
         Pair<Double,Double> results = mannWhitneyUTest(context);
-        return String.format("V: %.2f\tP: %.2e\tQ: %d",results.first,results.second,(int)Math.floor(QualityUtils.phredScaleErrorRate(results.second)));
+        return String.format("V: %.2f\tP: %.2e\tQ: %d",results.first,results.second,pToQ(results.second));
     }
 
     public static Pair<Double,Double> mannWhitneyUTest(UStatistic context) {

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.association;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.*;
 
@@ -40,41 +41,23 @@ public class RegionalAssociationHandler {
 
     /**
      * Switches what formatting to use based on wiggle or standard
-     * @param wiggleFormat - use wiggle format (just Q) or standard (S: P: Q:)
+     * @param bedGraphFormat - use bedgraph format (s p q) or standard (S: s P: p Q: q)
      * @return - test results in proper format
      */
-    public Map<AssociationContext,String> runTests(boolean wiggleFormat) {
+    public Map<AssociationContext,String> runTests(boolean bedGraphFormat) {
-        if ( wiggleFormat ) {
-            return runWiggleTests();
-        } else {
-            return runTests();
-        }
-    }
-
-    public Map<AssociationContext,String> runWiggleTests() {
-        // todo -- maybe the tdf should be the whole window rather than just the most recent loc?
-        Map<AssociationContext,String> testResults = new HashMap<AssociationContext,String>(associations.size());
-        for ( AssociationContext w : associations ) {
-            if ( w.isFull() ) {
-                testResults.put(w,String.format("%d",AssociationTestRunner.getQValue(w)));
-                w.slide();
-            }
-        }
-        return testResults;
-    }
-
-    /**
-     * For those AssociationContexts with full windows:
-     *  1) Run their associated test(s)
-     *  2) Slide the windows
-     */
-    public Map<AssociationContext,String> runTests() {
         // todo -- maybe the tdf should be the whole window rather than just the most recent loc?
         Map<AssociationContext,String> testResults = new HashMap<AssociationContext,String>(associations.size());
         for ( AssociationContext w : associations ) {
             if ( w.isFull() ) {
+                String outVal;
+                if ( bedGraphFormat ) {
+                    Pair<Double,Pair<Double,Integer>> vals = AssociationTestRunner.getTestValues(w);
+                    outVal = String.format("%.2f\t%.2e\t%d",vals.first,vals.second.first,vals.second.second);
+                } else {
+                    outVal = AssociationTestRunner.runTests(w);
+                }
                 testResults.put(w,String.format("%s\t%d\t%d\t%s",maps.getReferenceContext().getLocus().getContig(),
-                        maps.getReferenceContext().getLocus().getStart(),maps.getReferenceContext().getLocus().getStart()+1,AssociationTestRunner.runTests(w)));
+                        maps.getReferenceContext().getLocus().getStart()-w.getWindowSize()-1,maps.getReferenceContext().getLocus().getStart()+1, outVal));
                 w.slide();
             }
         }

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

@@ -16,12 +16,12 @@ import java.util.*;
 public class RegionalAssociationMultiplexer implements Multiplexer<Class<? extends AssociationContext>> {
 
     Set<Class<? extends AssociationContext>> contexts = null;
-    boolean wigOut = false;
+    boolean bedGraphOut = false;
 
     public RegionalAssociationMultiplexer(String[] toUse, boolean wiggleOutput) {
         super();
         contexts = getAssociations(toUse);
-        wigOut = wiggleOutput;
+        bedGraphOut = wiggleOutput;
     }
 
     public Collection<Class<? extends AssociationContext>> multiplex() {
@@ -29,8 +29,8 @@ public class RegionalAssociationMultiplexer implements Multiplexer<Class<? exten
     }
 
     public String transformArgument(final Class<? extends AssociationContext> context, String arg) {
-        if ( wigOut ) {
+        if ( bedGraphOut ) {
-            return String.format("%s.%s.wig",arg,context.getSimpleName());
+            return String.format("%s.%s.bedgraph",arg,context.getSimpleName());
         }
         return String.format("%s.%s.tdf", arg, context.getSimpleName());
     }

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

@@ -31,22 +31,19 @@ import java.util.*;
 public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAssociationHandler> implements TreeReducible<RegionalAssociationHandler> {
     @Argument(doc="Association type(s) to use. Supports multiple arguments (-AT thing1 -AT thing2).",shortName="AT",fullName="associationType",required=false)
     public String[] associationsToUse = null;
-    @Argument(doc="Change output file to wiggle format (will only see phred-scaled Q values, not STAT: x P: y Q: z",shortName="w",fullName="wiggle",required=false)
+    @Argument(doc="Change output file to bedgraph format (s p q, not STAT: s P: p Q: q",shortName="bg",fullName="bedgraph",required=false)
-    public boolean wiggleFormat = false;
+    public boolean bedGraph = false;
 
     @Output
-    @Multiplex(value=RegionalAssociationMultiplexer.class,arguments={"associationsToUse","wiggleFormat"})
+    @Multiplex(value=RegionalAssociationMultiplexer.class,arguments={"associationsToUse","bedGraph"})
     Map<AssociationContext,PrintStream> out;
 
     public void initialize() {
-        if ( wiggleFormat && getToolkit().getIntervals().size() > 1 ) {
-            throw new UserException("Wiggle format (fixedStep) is only consistent with a contiguous region (one interval) on one contig. Otherwise use the default output.");
-        }
 
         Set<AssociationContext> validAssociations = getAssociations();
 
-        if ( wiggleFormat ) {
+        if ( bedGraph ) {
-            writeWiggleHeaders(validAssociations);
+            writeBedGraphHeaders(validAssociations);
         }
     }
 
@@ -68,7 +65,7 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
         } catch (Exception e) {
             throw new StingException("Error in map reduce",e);
         }
-        Map<AssociationContext,String> testsHere = rac.runTests(wiggleFormat);
+        Map<AssociationContext,String> testsHere = rac.runTests(bedGraph);
         // todo -- really awful shitty formatting
         if ( testsHere.size() > 0 ) {
             for ( Map.Entry<AssociationContext,String> result : testsHere.entrySet() ) {
@@ -132,10 +129,10 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
         return getToolkit().getSAMFileSamples();
     }
 
-    public void writeWiggleHeaders(Set<AssociationContext> cons) {
+    public void writeBedGraphHeaders(Set<AssociationContext> cons) {
         for ( AssociationContext con : cons ) {
             GenomeLoc first = getToolkit().getIntervals().iterator().next();
-            String header = String.format("fixedStep chrom=%s start=%d step=%d span=%d",first.getContig(),first.getStart(),con.slideByValue(),con.getWindowSize());
+            String header = String.format("track type=bedGraph name=%s",con.getClass().getSimpleName());
             out.get(con.getClass()).printf("%s%n",header);
         }
     }