Extracts a Fastq file and the SQ tags to a separate file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@369 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,75 @@
+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.cmdLine.Argument;
+import net.sf.samtools.SAMRecord;
+
+import java.io.*;
+
+public class SAMToFastqAndSqWalker extends ReadWalker<Integer, Integer> {
+    @Argument(fullName="FASTQFILE", doc="Output path for Fastq file")
+    public File FASTQFILE;
+
+    @Argument(fullName="SQFILE", shortName="SQ", doc="Output path for secondary quality map (readName => SAM SQ field)", required=false)
+    public File SQFILE;
+
+    private PrintWriter fastqbw;
+    private PrintWriter sqbw;
+
+    private boolean ready = false;
+    
+    public Integer map(LocusContext context, SAMRecord read) {
+        if (!ready) {
+            try {
+                fastqbw = new PrintWriter(FASTQFILE);
+
+                if (SQFILE != null) {
+                    sqbw = new PrintWriter(SQFILE);
+                }
+
+                ready = true;
+            } catch (IOException e) {
+                err.println("Unable to open output files.");
+                System.exit(1);
+            }
+        }
+
+        String bases = read.getReadString();
+        String quals = read.getBaseQualityString();
+        byte[] sqs   = (byte[]) read.getAttribute("SQ");
+
+        fastqbw.println("@" + read.getReadName());
+        fastqbw.println(bases);
+
+        fastqbw.println("+" + read.getReadName());
+        fastqbw.println(quals);
+
+        if (sqbw != null && sqs != null) {
+            sqbw.print(read.getReadName() + "\t" + "SQ:H:");
+
+            for (byte sq : sqs) {
+                sqbw.printf("%02X", sq);
+            }
+            sqbw.println();
+        }
+
+        return null;
+    }
+
+    public Integer reduceInit() {
+        return null;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+
+    public void onTraversalDone(Integer sum) {
+        fastqbw.close();
+
+        if (sqbw != null) {
+            sqbw.close();
+        }
+    }
+}