Mismatch counter

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@62 348d0f76-0448-11de-a6fe-93d51630548a

playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchCounterWalker.java

@@ -0,0 +1,41 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.Utils;
+import edu.mit.broad.picard.reference.ReferenceSequence;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class MismatchCounterWalker extends BasicReadWalker<Integer, Integer> {
+    public Integer map(LocusContext context, SAMRecord read) {
+        int nMismatches = 0;
+        
+        ReferenceSequence refseq = context.getReferenceContig();
+
+        int start = read.getAlignmentStart()-1;
+        int stop  = read.getAlignmentEnd();
+        if ( read.getAlignmentBlocks().size() == 1 ) {
+            // No indels
+            List<Byte> refSeq = Utils.subseq(context.getReferenceContig().getBases(), start, stop);
+            List<Byte> readBases = Utils.subseq(read.getReadBases());
+
+            assert(refSeq.size() == readBases.size());
+
+            System.out.printf("start, stop = %d %d%n", start, stop);
+            System.out.println(read.format());
+            System.out.println(Utils.baseList2string(refSeq));
+            System.out.println(Utils.baseList2string(readBases));
+        }
+
+        return nMismatches;
+    }
+
+    public Integer reduceInit() { return 0; }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+}