FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations

-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.

public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java

@@ -28,6 +28,7 @@ public abstract class ReadFilter implements SamRecordFilter {
      * @return true if the SAMRecords matches the filter, otherwise false
      * @throws UnsupportedOperationException when paired filter not implemented
      */
+    @Override
     public boolean filterOut(final SAMRecord first, final SAMRecord second) {
         throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass());
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -258,9 +258,6 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                 if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
                     continue;
 
-                if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 )
-                    continue; // todo -- fixme, should take filtered context!
-
                 Allele base = Allele.create(p.getBase(), false);
                 boolean isFW = !p.getRead().getReadNegativeStrandFlag();