Added a walker to convert a bam file to fastq format (including the option to re-reverse the negative strand reads).

Picard has such a tool but it is geared towards their pipeline and requires intimate knowledge of the lanes/flowcells,etc.  This is just easy.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1413 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java

@@ -0,0 +1,43 @@
+package org.broadinstitute.sting.playground.gatk.walkers.fasta;
+
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import net.sf.samtools.SAMRecord;
+
+// create a fastq file from a bam file
+
+@WalkerName("BamToFastq")
+public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
+
+    @Argument(fullName="re_reverse", shortName="reverse", doc="re-reverse bases and quals of reads from the negative strand", required=false)
+    private Boolean RE_REVERSE = false;
+
+	public Integer map(char[] ref, SAMRecord read) {
+        out.println("@" + read.getReadName());
+        if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
+            out.println(read.getReadString());
+            out.println("+");
+            out.println(read.getBaseQualityString());
+        } else {
+            out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
+            out.println("+");
+            out.println(BaseUtils.simpleReverseComplement(read.getBaseQualityString()));
+        }
+
+        return 1;
+	}
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+	public Integer reduce(Integer value, Integer sum) {
+		return value + sum;
+	}
+
+    public void onTraversalDone(Integer sum) {
+        logger.info("Number of reads converted: " + sum);
+    }
+}