-Added mapping quality zero filter

-Set some reasonable defaults (based on pilot2)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1388 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java

@@ -10,7 +10,8 @@ import org.broadinstitute.sting.utils.GenotypeUtils;
 public class VECAlleleBalance implements VariantExclusionCriterion {  //extends RatioFilter {
     //final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed;
     private boolean exclude;
-    private double lowThreshold, highThreshold, ratio;
+    private double lowThreshold = 0.1, highThreshold = 0.85;
+    private double ratio;
 
     public void initialize(String arguments) {
         if (arguments != null && !arguments.isEmpty()) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQualityZero.java

@@ -0,0 +1,45 @@
+package org.broadinstitute.sting.playground.gatk.walkers.variants;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.rodVariants;
+import org.broadinstitute.sting.utils.MathUtils;
+import net.sf.samtools.SAMRecord;
+
+import java.util.List;
+
+
+public class VECMappingQualityZero implements VariantExclusionCriterion {
+    private int maximum = 50;
+    private int mq0Count;
+    private boolean exclude;
+
+    public void initialize(String arguments) {
+        if (arguments != null && !arguments.isEmpty()) {
+            maximum = Integer.valueOf(arguments);
+        }
+    }
+
+    public void compute(char ref, AlignmentContext context, rodVariants variant) {
+        List<SAMRecord> reads = context.getReads();
+        mq0Count = 0;
+        for (int i=0; i < reads.size(); i++) {
+            if ( reads.get(i).getMappingQuality() == 0 )
+                mq0Count++;
+        }
+        exclude = mq0Count > maximum;
+    }
+
+    public boolean isExcludable() {
+        return exclude;
+    }
+
+    public String getStudyHeader() {
+        return "MappingQualityZero("+maximum+")\tMQ0_count";
+    }
+
+    public String getStudyInfo() {
+        return (exclude ? "fail" : "pass") + "\t" + mq0Count;
+    }
+
+    public boolean useZeroQualityReads() { return true; }
+}

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java

@@ -7,7 +7,8 @@ import org.broadinstitute.sting.utils.*;
 public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // extends RatioFilter {
     //final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.LeftTailed;
     private boolean exclude;
-    private double threshold, ratio;
+    private double threshold = 0.0;
+    private double ratio;
 
     public void initialize(String arguments) {
         if (arguments != null && !arguments.isEmpty()) {