allow filters to specify whether they want to work with mapping quality zero reads; the VariantFiltrationWalker passes in the appropriate contextual reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1333 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -254,6 +254,8 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
     protected abstract boolean applyToVariant(rodVariants variant);
     protected abstract Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, rodVariants variant);
 
+    public boolean useZeroQualityReads() { return false; }
+
     public boolean exclude(char ref, LocusContext context, rodVariants variant) {
         boolean exclude = false;
 

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

@@ -19,6 +19,8 @@ public class VECDepthOfCoverage implements VariantExclusionCriterion {
         }
     }
 
+    public boolean useZeroQualityReads() { return false; }
+
     public boolean exclude(char ref, LocusContext context, rodVariants variant) {
         return context.getReads().size() > maximum;
     }

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

@@ -30,6 +30,8 @@ public class VECFisherStrand implements VariantExclusionCriterion {
         return false;
     }
 
+    public boolean useZeroQualityReads() { return false; }
+
     public static boolean strandTest(char ref, LocusContext context, int allele1, int allele2, double threshold, StringBuffer out) {
         int[][] table = getContingencyTable(context, allele1, allele2);
         if ( !variantIsHet(table) )
@@ -81,7 +83,7 @@ public class VECFisherStrand implements VariantExclusionCriterion {
         return ((table[0][1] != 0 || table[0][1] != 0) && (table[1][0] != 0 || table[1][1] != 0));
     }
 
-    private void printTable(int[][] table, double pValue) {
+    private static void printTable(int[][] table, double pValue) {
         System.out.printf("%d %d; %d %d : %f\n", table[0][0], table[0][1], table[1][0], table[1][1], pValue);
     }
 

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

@@ -12,6 +12,8 @@ public class VECLodThreshold implements VariantExclusionCriterion {
         }
     }
 
+    public boolean useZeroQualityReads() { return false; }
+
     public boolean exclude(char ref, LocusContext context, rodVariants variant) {
         return (variant.getLodBtr() < lodThreshold);
     }

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

@@ -7,4 +7,5 @@ public interface VariantExclusionCriterion {
     public void initialize(String arguments);
 
     public boolean exclude(char ref, LocusContext context, rodVariants variant);
+    public boolean useZeroQualityReads();
 }

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

@@ -18,6 +18,8 @@ import java.io.FileNotFoundException;
 import java.io.PrintWriter;
 import java.util.*;
 
+import net.sf.samtools.SAMRecord;
+
 /**
  * VariantFiltrationWalker applies specified conditionally independent features to pre-called variants, thus modifying
  * the likelihoods of each genotype.  At the moment, the variants are expected to be in gelitext format.
@@ -191,8 +193,12 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
             // Apply exclusion tests that accept or reject the variant call
             ArrayList<String> exclusionResults = new ArrayList<String>();
 
+            // we need to provide an alternative context without mapping quality 0 reads
+            // for those exclusion criterion that don't want them
+            LocusContext Q0freeContext = removeQ0reads(context);
+
             for ( VariantExclusionCriterion vec : requestedExclusions ) {
-                boolean excludeResult = vec.exclude(ref, context, variant);
+                boolean excludeResult = vec.exclude(ref, (vec.useZeroQualityReads() ? context : Q0freeContext), variant);
 
                 if (excludeResult) {
                     exclusionResults.add(rationalizeClassName(vec.getClass()));
@@ -223,6 +229,28 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
         return 0;
     }
 
+    private LocusContext removeQ0reads(LocusContext context) {
+        // set up the variables
+        List<SAMRecord> reads = context.getReads();
+        List<Integer> offsets = context.getOffsets();
+        Iterator<SAMRecord> readIter = reads.iterator();
+        Iterator<Integer> offsetIter = offsets.iterator();
+        ArrayList<SAMRecord> Q0freeReads = new ArrayList<SAMRecord>();
+        ArrayList<Integer> Q0freeOffsets = new ArrayList<Integer>();
+
+        // copy over good reads/offsets
+        while ( readIter.hasNext() ) {
+            SAMRecord read = readIter.next();
+            Integer offset = offsetIter.next();
+            if ( read.getMappingQuality() > 0 ) {
+                Q0freeReads.add(read);
+                Q0freeOffsets.add(offset);
+            }                       
+        }
+        
+        return new LocusContext(context.getLocation(), Q0freeReads, Q0freeOffsets);    
+    }
+
     /**
      * Increment the number of loci processed.
      *