Output format is 10^6 times better - now uses the multiplexer to write tdf tracks that can (after conversion to binary with igvtools) can be loaded directly into igv.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5381 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -23,7 +23,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 public class AssociationTestRunner {
     static Normal standardNormal = new Normal(0.0,1.0,null);
 
-    public static List<String> runTests(AssociationContext context) {
+    public static String runTests(AssociationContext context) {
         List<String> results = new ArrayList<String>();
         if ( context instanceof TStatistic) {
             results.add(runStudentT((TStatistic) context));
@@ -37,7 +37,16 @@ public class AssociationTestRunner {
             results.add(runU((UStatistic) context));
         }
 
-        return results;
+        StringBuffer buf = new StringBuffer();
+        if ( results.size() > 0 ) {
+            buf.append(results.remove(0));
+            for ( String s : results ) {
+                buf.append('\t');
+                buf.append(s);
+            }
+        }
+
+        return buf.toString();
     }
 
     public static String runStudentT(TStatistic context) {

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

@@ -43,11 +43,13 @@ public class RegionalAssociationHandler {
      *  1) Run their associated test(s)
      *  2) Slide the windows
      */
-    public List<String> runTests() {
-        List<String> testResults = new ArrayList<String>(associations.size());
+    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() ) {
-                testResults.addAll(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().getStop(),AssociationTestRunner.runTests(w)));
                 w.slide();
             }
         }

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

@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association;
+
+import org.broadinstitute.sting.gatk.walkers.Multiplexer;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 3/6/11
+ * Time: 12:09 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class RegionalAssociationMultiplexer implements Multiplexer<Class<? extends AssociationContext>> {
+
+    Set<Class<? extends AssociationContext>> contexts = null;
+
+    public RegionalAssociationMultiplexer(String[] toUse) {
+        super();
+        contexts = getAssociations(toUse);
+
+    }
+
+    public Collection<Class<? extends AssociationContext>> multiplex() {
+        return contexts;
+    }
+
+    public String transformArgument(final Class<? extends AssociationContext> context, String arg) {
+        return String.format("%s.%s.tdf", arg, context.getSimpleName());
+    }
+
+    private Set<Class<? extends AssociationContext>> getAssociations(String[] associationsToUse) {
+        List<Class<? extends AssociationContext>> contexts = new PluginManager<AssociationContext>(AssociationContext.class).getPlugins();
+        Map<String,Class<? extends AssociationContext>> classNameToClass = new HashMap<String,Class<? extends AssociationContext>>(contexts.size());
+        for ( Class<? extends AssociationContext> clazz : contexts ) {
+            classNameToClass.put(clazz.getSimpleName(),clazz);
+        }
+
+        Set<Class<? extends AssociationContext>> validAssociations = new HashSet<Class<? extends AssociationContext>>();
+        for ( String s : associationsToUse ) {
+            validAssociations.add(classNameToClass.get(s));
+        }
+        return validAssociations;
+    }
+}

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

@@ -7,11 +7,13 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.wiggle.WiggleWriter;
 
 import java.io.PrintStream;
 import java.lang.reflect.Modifier;
@@ -27,7 +29,8 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
     public String[] associationsToUse = null;
 
     @Output
-    PrintStream out;
+    @Multiplex(value=RegionalAssociationMultiplexer.class,arguments={"associationsToUse"})
+    Map<AssociationContext,PrintStream> out;
 
     public RegionalAssociationHandler reduceInit() {
         Set<AssociationContext> validAssociations = getAssociations();
@@ -47,17 +50,17 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
         } catch (Exception e) {
             throw new StingException("Error in map reduce",e);
         }
-        List<String> testsHere = rac.runTests();
+        Map<AssociationContext,String> testsHere = rac.runTests();
         // todo -- really awful shitty formatting
         if ( testsHere.size() > 0 ) {
-            out.printf("%s%n",rac.getLocation().toString());
-            for ( String s : testsHere ) {
-                out.printf("%s%n",s);
+            for ( Map.Entry<AssociationContext,String> result : testsHere.entrySet() ) {
+                out.get(result.getKey().getClass()).printf("%s%n",result.getValue());
             }
         }
         return rac;
     }
-    private Set<AssociationContext> getAssociations() {
+
+    public Set<AssociationContext> getAssociations() {
         List<Class<? extends AssociationContext>> contexts = new PluginManager<AssociationContext>(AssociationContext.class).getPlugins();
         Map<String,Class<? extends AssociationContext>> classNameToClass = new HashMap<String,Class<? extends AssociationContext>>(contexts.size());
         for ( Class<? extends AssociationContext> clazz : contexts ) {