Added a module to test for reference mismatch associations, and a self-normalized/self-normalizing version.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5408 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,91 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+
+import org.broadinstitute.sting.gatk.datasources.sample.Sample;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.RegionalAssociationWalker;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 3/8/11
+ * Time: 2:32 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class MismatchRate extends UStatistic {
+
+    private Map<Sample,Object> sampleStats = new HashMap<Sample,Object>();
+    private int currentRefBase = 0;
+
+    public void init(RegionalAssociationWalker walker) {
+        Set<Sample> samples = walker.getSamples();
+        for ( Sample s : samples ) {
+            if ( s.hasProperty("mismatch_rate.mean") && s.hasProperty("mismatch_rate.std") ) {
+                double mn = (Double) s.getProperty("mismatch_rate.mean");
+                double std = (Double) s.getProperty("mismatch_rate.std");
+                sampleStats.put(s,new Pair<Double,Double>(mn,std));
+            } else {
+                sampleStats.put(s,new MathUtils.RunningAverage());
+            }
+        }
+    }
+
+    @Override
+    public Map<Sample,Object> mapLocus(MapExtender extender) {
+        currentRefBase = BaseUtils.simpleBaseToBaseIndex(extender.getReferenceContext().getBase());
+        Map<Sample,ReadBackedPileup> pileups = extender.getReadFilteredPileup();
+        Map<Sample,Object> maps = new HashMap<Sample,Object>(pileups.size());
+        for ( Map.Entry<Sample,ReadBackedPileup> samPileup : pileups.entrySet() ) {
+            maps.put(samPileup.getKey(),map(samPileup.getKey(),samPileup.getValue()));
+        }
+
+        return maps;
+    }
+
+    public Collection<Number> map(Sample sample, ReadBackedPileup pileup) {
+        Object stats = sampleStats.get(sample);
+        double mn;
+        double std;
+        if ( stats instanceof Pair ) {
+            mn = ((Pair<Double,Double>)stats).first;
+            std = ((Pair<Double,Double>)stats).second;
+        } else {
+            MathUtils.RunningAverage ra = (MathUtils.RunningAverage) stats;
+            mn = ra.mean();
+            std = ra.stddev();
+            if ( std <= 0.0 ) {
+                std = 1.0;
+            }
+            ra.add(pileup.size());
+        }
+
+        return Arrays.asList((Number) ((calcMMR(pileup) - mn) / std));
+    }
+
+    public double calcMMR(ReadBackedPileup rbp) {
+        int[] counts = rbp.getBaseCounts();
+        int total = 0;
+        int nonref = 0;
+        for ( int base : new int[]{0,1,2,3} ) {
+            total += counts[base];
+            if ( base != currentRefBase ) {
+                nonref += counts[base];
+            }
+        }
+
+        return ((double)nonref)/total;
+    }
+
+    // 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 100; }
+    public int slideByValue() { return 10; }
+    public boolean usePreviouslySeenReads() { return true; }
+}

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

@@ -0,0 +1,48 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+
+import org.broadinstitute.sting.gatk.datasources.sample.Sample;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+import java.util.Map;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 3/8/11
+ * Time: 1:17 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ReferenceMismatches extends ZStatistic {
+
+    final static int[] BASE_INDEX = {0,1,2,3};
+
+    int currentRefBase = 0;
+
+    @Override
+    public Map<Sample,Object> mapLocus(MapExtender extender) {
+        currentRefBase = BaseUtils.simpleBaseToBaseIndex(extender.getReferenceContext().getBase());
+        return super.mapLocus(extender);
+    }
+
+    public Pair<Number,Number> map(ReadBackedPileup rbp) {
+        int[] counts = rbp.getBaseCounts();
+        int total = 0;
+        int nonref = 0;
+        for ( int base : BASE_INDEX ) {
+            total += counts[base];
+            if ( base != currentRefBase ) {
+                nonref += counts[base];
+            }
+        }
+
+        return new Pair<Number,Number>(nonref,total);
+    }
+
+    public int getWindowSize() { return 100; }
+    public int slideByValue() { return 25; }
+    public boolean usePreviouslySeenReads() { return true; }
+}