From e91a429c585b292a4dd7e768ffd86ab5adb700d3 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 13 Apr 2009 15:29:55 +0000
Subject: [PATCH] A class to print out as much context about the given locus
 site as is possible.  Useful for testing traversal engines -- run old and new
 code across a given region and diff the output to make sure they have the
 same context.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/PrintLocusContextWalker.java | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java
new file mode 100755
index 000000000..2aa556734
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java
@@ -0,0 +1,45 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+
+import java.util.List;
+import java.util.Arrays;
+import java.util.ArrayList;
+
+import net.sf.samtools.SAMRecord;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: hanna
+ * Date: 13 Apr, 2009
+ * Time: 11:23:14 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer> {
+    public LocusContext map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        out.printf( "In map: ref = %c, loc = %s, reads = %s%n", ref,
+                                                                context.getLocation(),
+                                                                Arrays.deepToString( getReadNames(context.getReads()) ) );
+        return context;
+    }
+
+    public Integer reduceInit() { return 0; }
+
+    public Integer reduce(LocusContext context, Integer sum) {
+        out.printf( "In reduce: loc = %s, reads = %s, sum =%d%n", context.getLocation(),
+                                                                  Arrays.deepToString( getReadNames(context.getReads()) ),
+                                                                  sum );
+
+
+        return sum + 1;
+    }
+
+    private String[] getReadNames( List<SAMRecord> reads ) {
+        String[] readNames = new String[ reads.size() ];
+        for( int i = 0; i < reads.size(); i++ )
+            readNames[i] = reads.get(i).getReadName();
+        return readNames;
+    }
+}