added MAF-style output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1163 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/SomaticMutationWalker.java

@@ -50,6 +50,9 @@ public class  SomaticMutationWalker extends LocusWalker<Integer, Integer> {
 //    @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
     public boolean OUTPUT_FAILURES = true;
 
+    @Argument(fullName = "output_format", shortName = "s3", required = true, doc="Format of output: bed or maf")
+    public String OUTPUT_FORMAT;
+
 
     public void initialize() {
     }
@@ -260,6 +263,19 @@ public class  SomaticMutationWalker extends LocusWalker<Integer, Integer> {
 
             // if we're still here... we've got a somatic mutation!  Output the results
             // and stop looking for mutants!
+            if ("maf".equalsIgnoreCase(OUTPUT_FORMAT)) {
+                out.println(
+                       "36\t" + //build
+                        context.getContig() + "\t" +
+                        context.getPosition() + "\t" +
+                        context.getPosition() + "\t" +
+                        upRef + "\t" +
+                        upRef + "\t" +
+                        altAllele + "\t" +
+                        tumorSampleName + "\t" +
+                        normalSampleName);
+            } else {
+
                 String msg =
                             (failedMidpointCheck?"__FAILED-MPCHECK":"") +
                             "TScore:" + tumorLod +
@@ -277,6 +293,7 @@ public class  SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                                 context.getPosition() + "\t"
                         + msg.replace(' ','_')
                         );
+            }