Walker to print out a histogram of aligned reads per mismatches allowed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@76 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.LocusContext;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mdepristo
+ * Date: Feb 22, 2009
+ * Time: 3:22:14 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class AlignedReadsHistoWalker extends BasicReadWalker<Integer, Integer> {
+    long[] alignCounts = new long[51];
+
+    public void initialize() {
+        for ( int i = 0; i < this.alignCounts.length; i++ ) {
+            this.alignCounts[i] = 0;
+        }
+    }
+
+    public String walkerType() { return "ByRead"; }
+
+    // Do we actually want to operate on the context?
+    public boolean filter(LocusContext context, SAMRecord read) {
+	    // we only want aligned reads
+	    return !read.getReadUnmappedFlag();
+    }
+
+    // Map over the org.broadinstitute.sting.atk.LocusContext
+    public Integer map(LocusContext context, SAMRecord read) {
+        //System.out.println(read.getAttribute("NM"));
+        int editDist = Integer.parseInt(read.getAttribute("NM").toString());
+        this.alignCounts[editDist]++;
+        return 1;
+    }
+
+    // Given result of map function
+    public Integer reduceInit() { return 0; }
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    public void onTraversalDone() {
+        int curTotal = 0;
+        for ( int i = 0; i < this.alignCounts.length; i++ ) {
+            curTotal += alignCounts[i];
+            System.out.printf("%3d %10d%n", i, curTotal);
+        }
+    }
+}