From e410c005c0b1ec7da34676e0c06c026965b64602 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 12 Apr 2009 19:40:42 +0000
Subject: [PATCH] A debugging tool to ensure the SQ tag in a four-prob SAM file
 matches the SAMRecord strand orientation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@368 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/DisplayFourBaseReadWalker.java    | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/DisplayFourBaseReadWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DisplayFourBaseReadWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DisplayFourBaseReadWalker.java
new file mode 100644
index 000000000..e32fc2342
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DisplayFourBaseReadWalker.java
@@ -0,0 +1,58 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.QualityUtils;
+import net.sf.samtools.SAMRecord;
+
+public class DisplayFourBaseReadWalker extends ReadWalker<Integer, Integer> {
+    public Integer map(LocusContext context, SAMRecord read) {
+        String bases = read.getReadString();
+
+        boolean displayed = false;
+
+        byte[] sq = (byte[]) read.getAttribute("SQ");
+
+        if (read.getReadName().equalsIgnoreCase("30JJE.5.24197751")) {
+            System.out.println(read.format());
+        }
+
+        for (int i = 0; i < sq.length; i++) {
+            int baseIndex = QualityUtils.compressedQualityToBaseIndex(sq[i]);
+            char base = '.';
+            switch (baseIndex) {
+                case 0: base = 'A'; break;
+                case 1: base = 'C'; break;
+                case 2: base = 'G'; break;
+                case 3: base = 'T'; break;
+            }
+
+            if (base == bases.charAt(i)) {
+                if (!displayed) {
+                    System.out.println(bases);
+                    displayed = true;
+                }
+                
+                System.out.print(base);
+            }
+            else {
+                if (displayed) {
+                    System.out.print(" ");
+                }
+            }
+        }
+        if (displayed) {
+            System.out.print("\n");
+        }
+
+        return 0;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return 0;
+    }
+}