A pass at a sample-normalized test. I think maybe all of them will simply do their own normalizing.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5367 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 15:42:25 +00:00 · 2011-03-03 15:42:25 +00:00 · 835a26d145
parent ef38fd1e0e
commit 835a26d145
1 changed files with 76 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/SampleDepth.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/SampleDepth.java
@ -0,0 +1,76 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+
+import org.broadinstitute.sting.gatk.datasources.sample.Sample;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.RegionalAssociationWalker;
+import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+import java.util.*;
+
+/**
+ * @author chartl
+ */
+public class SampleDepth extends UStatistic {
+
+    public Map<Sample,Object> sampleStats = null;
+
+    public SampleDepth() {
+        super();
+        sampleStats = new HashMap<Sample,Object>();
+    }
+
+    // either: the user associates data with the sample (doc.mean, doc.std)
+    //        >OR we calculate the values on-the-fly (e.g. running mean/stdev)
+    public void init(RegionalAssociationWalker walker) {
+        Set<Sample> samples = walker.getSamples();
+        for ( Sample s : samples ) {
+            if ( s.hasProperty("doc.mean") && s.hasProperty("doc.std") ) {
+                double mn = Double.parseDouble((String) s.getProperty("doc.mean"));
+                double std = Double.parseDouble((String) s.getProperty("doc.std"));
+                sampleStats.put(s,new Pair<Double,Double>(mn,std));
+            } else {
+                sampleStats.put(s,new MathUtils.RunningAverage());
+            }
+        }
+    }
+
+    public Collection<Number> map(ReadBackedPileup pileup) {
+        Collection<Sample> samples = pileup.getSamples();
+        Sample sample;
+        if ( samples.size() > 1 ) {
+            throw new StingException("Multiple samples inside a sample-specific pileup");
+        } else if ( samples.size() == 0 ) {
+            return Arrays.asList();
+        } else {
+            sample = samples.iterator().next();
+        }
+        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)((pileup.size()-mn)/std));
+    }
+
+    public int getWindowSize() { return 25; }
+    public int slideByValue() { return 5; }
+    public boolean usePreviouslySeenReads() { return true; }
+
+
+}