A very simple walker to print out (using the ROD's toString method) all of

the RODs it sees.  This is the easiest solution to get around the (temporary)
bug of reads being seen multiple times by reads walkers when close intervals
are passed to them (i.e. process full contigs and then use a ref walker to
filter the ones within your intervals of choice)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1273 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.walkers.*;
+
+/**
+ * PrintRODsWalker prints out all of the RODs that it sees (using the ROD's toString method)
+ */
+@Requires(value={DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=ReferenceOrderedDatum.class))
+public class PrintRODsWalker extends RefWalker<Integer, Integer> {
+
+    /**
+     * Initialize the number of loci processed to zero.
+     *
+     * @return 0
+     */
+    public Integer reduceInit() { return 0; }
+
+    /**
+     * For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
+     *
+     * @param tracker  the meta-data tracker
+     * @param ref      the reference base
+     * @param context  the context for the given locus
+     * @return 1 if the locus was successfully processed, 0 if otherwise
+     */
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        ReferenceOrderedDatum variant = tracker.lookup("variant", null);
+
+        if (variant != null )
+            out.println(variant);
+
+        return 1;
+    }
+
+    /**
+     * Increment the number of rods processed.
+     *
+     * @param value result of the map.
+     * @param sum   accumulator for the reduce.
+     * @return the new number of rods processed.
+     */
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+}