Making SplitReads output FastQ's instead of BAM

- eliminates one step in my pipeline
   - BAM is too finicky and maintaining parameters that wouldn't be useful was becoming a headache, better avoided.

public/java/src/org/broadinstitute/sting/gatk/io/FastqFileWriter.java

@@ -0,0 +1,77 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.io;
+
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+
+/**
+ * User: carneiro
+ * Date: 1/27/13
+ * Time: 12:54 AM
+ */
+public class FastqFileWriter {
+    private PrintStream output;
+
+    public FastqFileWriter(String filename) {
+        try {
+            this.output = new PrintStream(filename);
+        } catch (FileNotFoundException e) {
+            throw new ReviewedStingException("Can't open file " + filename);
+        }
+    }
+
+    public void addAlignment(GATKSAMRecord read) {
+        output.println("@" + read.getReadName());
+
+        if (read.getReadNegativeStrandFlag()) {
+            output.println(ReadUtils.getBasesReverseComplement(read));
+            output.println("+");
+            output.println(ReadUtils.convertReadQualToString(invertQuals(read.getBaseQualities())));
+        } else {
+            output.println(ReadUtils.convertReadBasesToString(read));
+            output.println("+");
+            output.println(ReadUtils.convertReadQualToString(read));
+        }
+    }
+
+    public void close() {
+        this.output.close();
+    }
+
+    private byte[] invertQuals (byte[] quals) {
+        final int l = quals.length;
+        byte[] invertedQuals = new byte[l];
+        for (int i=0; i<l; i++) {
+            invertedQuals[l-1-i] = quals[i];
+        }
+        return invertedQuals;
+    }
+}

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -31,10 +31,7 @@ import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.recalibration.EventType;
 
-import java.util.Arrays;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
 /**
  * @author ebanks, depristo
@@ -137,6 +134,13 @@ public class GATKSAMRecord extends BAMRecord {
                 flags, readLen, mateReferenceSequenceIndex, mateAlignmentStart, insertSize, variableLengthBlock);
     }
 
+    public static GATKSAMRecord createRandomRead(int length) {
+        List<CigarElement> cigarElements = new LinkedList<CigarElement>();
+        cigarElements.add(new CigarElement(length, CigarOperator.M));
+        Cigar cigar = new Cigar(cigarElements);
+        return ArtificialSAMUtils.createArtificialRead(cigar);
+    }
+
     ///////////////////////////////////////////////////////////////////////////////
     // *** The following methods are overloaded to cache the appropriate data ***//
     ///////////////////////////////////////////////////////////////////////////////

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.variant.utils.BaseUtils;
 
 import java.io.File;
 import java.util.*;
@@ -850,4 +851,66 @@ public class ReadUtils {
         return events;
     }
 
+    /**
+     * Given a read, outputs the read bases in a string format
+     *
+     * @param read the read
+     * @return a string representation of the read bases
+     */
+    public static String convertReadBasesToString(GATKSAMRecord read) {
+        String bases = "";
+        for (byte b : read.getReadBases()) {
+            bases += (char) b;
+        }
+        return bases.toUpperCase();
+    }
+
+    /**
+     * Given a read, outputs the base qualities in a string format
+     *
+     * @param quals the read qualities
+     * @return a string representation of the base qualities
+     */
+    public static String convertReadQualToString(byte[] quals) {
+        String result = "";
+        for (byte b : quals) {
+            result += (char) (33 + b);
+        }
+        return result;
+    }
+
+    /**
+     * Given a read, outputs the base qualities in a string format
+     *
+     * @param read the read
+     * @return a string representation of the base qualities
+     */
+    public static String convertReadQualToString(GATKSAMRecord read) {
+        return convertReadQualToString(read.getBaseQualities());
+    }
+
+    /**
+     * Returns the reverse complement of the read bases
+     *
+     * @param bases the read bases
+     * @return the reverse complement of the read bases
+     */
+    public static String getBasesReverseComplement(byte[] bases) {
+        String reverse = "";
+        for (int i = bases.length-1; i >=0; i--) {
+            reverse += (char) BaseUtils.getComplement(bases[i]);
+        }
+        return reverse;
+    }
+
+    /**
+     * Returns the reverse complement of the read bases
+     *
+     * @param read the read
+     * @return the reverse complement of the read bases
+     */
+    public static String getBasesReverseComplement(GATKSAMRecord read) {
+        return getBasesReverseComplement(read.getReadBases());
+    }
+
 }

public/java/src/org/broadinstitute/variant/utils/BaseUtils.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.variant.utils;
 
 import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Arrays;
@@ -497,4 +498,26 @@ public class BaseUtils {
 
         return randomBaseIndex;
     }
+
+    public static byte getComplement(byte base) {
+        switch(base) {
+            case 'a':
+            case 'A':
+                return 'T';
+            case 'c':
+            case 'C':
+                return 'G';
+            case 'g':
+            case 'G':
+                return 'C';
+            case 't':
+            case 'T':
+                return 'A';
+            case 'n':
+            case 'N':
+                return 'N';
+            default:
+                throw new ReviewedStingException("base must be A, C, G or T. " + (char) base + " is not a valid base.");
+        }
+    }
 }

public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java

@@ -26,12 +26,15 @@
 package org.broadinstitute.sting.utils.sam;
 
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Random;
 
 
 public class ReadUtilsUnitTest extends BaseTest {
@@ -145,4 +148,21 @@ public class ReadUtilsUnitTest extends BaseTest {
         boundary = get.getAdaptor(read);
         Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
     }
+
+    @Test (enabled = true)
+    public void testGetBasesReverseComplement() {
+        int iterations = 1000;
+        Random random = GenomeAnalysisEngine.getRandomGenerator();
+        while(iterations-- > 0) {
+            final int l = random.nextInt(1000);
+            GATKSAMRecord read = GATKSAMRecord.createRandomRead(l);
+            byte [] original = read.getReadBases();
+            byte [] reconverted = new byte[l];
+            String revComp = ReadUtils.getBasesReverseComplement(read);
+            for (int i=0; i<l; i++) {
+                reconverted[l-1-i] = BaseUtils.getComplement((byte) revComp.charAt(i));
+            }
+            Assert.assertEquals(reconverted, original);
+        }
+    }
 }