Added a walker to help sort out which samples in a region are giving signal. Lots of reused code that shouldn't be. Will refactor later.

Also fixed an "issue" with InsertSizeDistribution -- apparently for mate pairs, the first mate (karyotypically) will have a POSITIVE insert size, and the second a NEGATIVE insert size -- thus the insert size distribution was being conflated with enrichment/depletion of first-in-pair or second-in-pair reads. Gah.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5623 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,123 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+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.oneoffprojects.walkers.association.AssociationContext;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.MapHolder;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.RegionalAssociationHandler;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
+import java.io.PrintStream;
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 4/12/11
+ * Time: 5:21 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class RAWSampleStats extends LocusWalker<MapHolder,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="Set the window size for associations to this value",shortName="w",fullName="window",required=false)
+    public int windowSize = 50;
+    @Argument(doc="Set the window sliding value for associations to this value",shortName="s",fullName="slide",required=false)
+    public int slideBy = 10;
+
+    @Output
+    PrintStream out;
+
+    public RegionalAssociationHandler reduceInit() {
+        return new RegionalAssociationHandler(getAssociations(),getToolkit().getSAMFileSamples(),false);
+    }
+
+    public MapHolder map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return new MapHolder(tracker,ref,context);
+    }
+
+    public RegionalAssociationHandler reduce(MapHolder holder, RegionalAssociationHandler handler) {
+        handler.updateExtender(holder);
+        StringBuffer contextBuf = new StringBuffer();
+        contextBuf.append(holder.getRef().getLocus().toString());
+        for ( AssociationContext context : handler.getAssociations() ) {
+            contextBuf.append("\t");
+            contextBuf.append(context.getClass().getSimpleName());
+            boolean first = true;
+            for ( Map.Entry<Sample,AlignmentContext> entry : handler.getExtender().getContext().entrySet() ) {
+                if ( ! first ) {
+                    contextBuf.append(";");
+                } else {
+                    first = false;
+                }
+                contextBuf.append(entry.getKey().getId());
+                contextBuf.append("=");
+                contextBuf.append(handleMap(context.map(entry.getValue().getBasePileup())));
+            }
+            contextBuf.append("\t");
+        }
+
+        out.printf("%s%n",contextBuf.toString());
+
+        return handler;
+    }
+
+    public String handleMap(Object o) {
+        if ( o instanceof Pair) {
+            Pair<Number,Number> k = (Pair<Number,Number>) o;
+            return String.format("%.2f",k.first.doubleValue()/k.second.doubleValue());
+        }
+
+        if ( o instanceof Collection ) {
+            Collection<Number> k = (Collection<Number>) o;
+            return String.format("%.2f", MathUtils.average(k,true));
+        }
+
+        return "NA";
+    }
+
+
+    public Set<AssociationContext> getAssociations() {
+        List<Class<? extends AssociationContext>> contexts = new PluginManager<AssociationContext>(AssociationContext.class).getPlugins();
+
+        if ( associationsToUse.length > 0 && associationsToUse[0].equals("ALL") ) {
+            HashSet<AssociationContext> allAssoc =  new HashSet<AssociationContext>(contexts.size());
+            for ( Class<? extends AssociationContext> clazz : contexts ) {
+                AssociationContext context;
+                try {
+                    context = clazz.getConstructor(new Class[] {}).newInstance(new Object[] {});
+                } catch (Exception e ) {
+                    throw new StingException("The class "+clazz.getSimpleName()+" could not be instantiated",e);
+                }
+                allAssoc.add(context);
+            }
+            return allAssoc;
+        }
+
+
+        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<AssociationContext> validAssociations = new HashSet<AssociationContext>();
+        for ( String s : associationsToUse ) {
+            AssociationContext context;
+            try {
+                context = classNameToClass.get(s).getConstructor(new Class[]{}).newInstance(new Object[] {});
+            } catch ( Exception e ) {
+                throw new StingException("The class "+s+" could not be instantiated.",e);
+            }
+            validAssociations.add(context);
+        }
+        return validAssociations;
+    }
+}

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

@@ -17,7 +17,7 @@ public class InsertSizeDistribution extends ValueTest {
     public Collection<Number> map(ReadBackedPileup pileup) {
         List<Integer> insertSizes = new ArrayList<Integer>(pileup.size());
         for ( PileupElement e : pileup ) {
-            insertSizes.add(e.getRead().getInferredInsertSize());
+            insertSizes.add(Math.abs(e.getRead().getInferredInsertSize()));
         }
 
         return (Collection) insertSizes;