From 311ab8da5ade7ebe77057cfa0226b4f0437ef557 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 14 Oct 2009 17:28:51 +0000
Subject: [PATCH] A helper class to create the masks for the sequenom design
 maker. This project is now officially done.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1834 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/fasta/CreateSequenomMask.java     | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
new file mode 100755
index 000000000..251c1fe5e
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
@@ -0,0 +1,43 @@
+package org.broadinstitute.sting.gatk.walkers.fasta;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.genotype.Variation;
+
+import java.util.Iterator;
+
+public class CreateSequenomMask extends RodWalker<Integer, Integer> {
+
+    public void initialize() {}
+
+	public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
+        int result = 0;
+
+        Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
+        while (rods.hasNext()) {
+            ReferenceOrderedDatum rod = rods.next();
+            if ( rod instanceof Variation && ((Variation)rod).isSNP() ) {
+                out.println(context.getLocation());
+                result = 1;
+                break;
+            }
+        }
+
+        return result;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+	public Integer reduce(Integer value, Integer sum) {
+		return value + sum;
+	}
+
+    public void onTraversalDone(Integer sum) {
+        logger.info("Found " + sum + " masking sites.");
+    }
+}
\ No newline at end of file