By default, VF should ask for deleted bases so that they show up in coverage.

The Strand filter then needs to ignore those bases when determining bias.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java

@@ -186,6 +186,10 @@ public class VECFisherStrand implements VariantExclusionCriterion {
             SAMRecord read = reads.get(readIndex);
             int offset = offsets.get(readIndex);
 
+	    // skip over deletion sites
+	    if ( offset == -1 )
+		continue;
+
             int readAllele = BaseUtils.simpleBaseToBaseIndex(read.getReadString().charAt(offset));
             boolean isFW = !read.getReadNegativeStrandFlag();
 

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -197,6 +197,14 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
      */
     public Integer reduceInit() { return 0; }
 
+    
+    /**
+     * We want reads that span deletions
+     *
+     * @return true
+     */
+    public boolean includeReadsWithDeletionAtLoci() { return true; }
+
     /**
      * For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
      *