From ebec0ec1719fbf82f1b9c94fd857ed76b778ea1f Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 12 Aug 2009 20:24:37 +0000
Subject: [PATCH] A standalone companion to BamToFastqWalker: does the same
 thing but without calling in gatk's heavy artillery (does not "require" a
 reference either). Extracts seqs and quals and places them into fastq; along
 the way it also reverse complements reads that align to the negative strand
 (so that fastq contains reads as they come from the machine).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1419 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/tools/BamToFastq.java    | 81 +++++++++++++++++++
 1 file changed, 81 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java

diff --git a/java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java b/java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java
new file mode 100644
index 000000000..f1080c065
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.playground.tools;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Option;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+
+import java.io.*;
+
+import org.broadinstitute.sting.utils.BaseUtils;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Aug 12, 2009
+ * Time: 3:24:46 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class BamToFastq extends CommandLineProgram {
+    @Usage(programVersion="1.0") public String USAGE = "Extracts read sequences and qualities from the input sam/bam file and wirtes them into "+
+        "the output file in fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, "+
+        "the read's sequence from input sam file will be reverse-complemented prior to writing it to fastq in order restore correctly "+
+        "the original read sequence as it was generated by the sequencer.";
+    @Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
+                optional=true) public File IN = null;
+    @Option(shortName="O",doc="Output file (fastq). If not specified, output is printed to stdout.",
+            optional=true) public File OUT = null;
+    @Option(shortName="RC", doc="re-reverse bases and quals of reads aligned to the negative strand before writing them to fastq", optional=true)
+            public Boolean RE_REVERSE = true;
+
+    public static void main(final String[] argv) {
+        System.exit(new BamToFastq().instanceMain(argv));
+    }
+
+    protected int doWork() {
+
+
+        InputStream ins = null;
+        if ( IN == null ) ins = System.in;
+        else {
+            try {
+                ins = new FileInputStream(IN);
+            } catch ( FileNotFoundException ie ) {
+                System.out.println("Failed to open input file "+IN+": "+ie.getCause());
+                return 1;
+            }
+        }
+
+        SAMFileReader inReader = new SAMFileReader(ins);
+        PrintStream out = null;
+        if ( OUT == null ) out = System.out;
+        else {
+            try {
+                out =  new PrintStream(OUT);
+            } catch ( FileNotFoundException ie ) {
+                System.out.println("Failed to open output file "+OUT+": "+ie.getCause());
+                return 1;
+            }
+        }
+
+        for (SAMRecord read : inReader ) {
+            out.println("@" + read.getReadName());
+            if ( read.getReadUnmappedFlag() || !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.reverse(read.getBaseQualityString()));
+            }
+        }
+        inReader.close();
+        out.close();
+
+        return 0;
+    }
+
+
+}