Refactoring FastqRecord

src/main/java/htsjdk/samtools/fastq/BasicFastqWriter.java

@@ -58,12 +58,10 @@ public BasicFastqWriter(final PrintStream writer) {
 
     @Override
     public void write(final FastqRecord rec) {
-        writer.print(FastqConstants.SEQUENCE_HEADER);
-        writer.println(rec.getReadHeader());
-        writer.println(rec.getReadString());
-        writer.print(FastqConstants.QUALITY_HEADER);
-        writer.println(rec.getBaseQualityHeader() == null ? "" : rec.getBaseQualityHeader());
-        writer.println(rec.getBaseQualityString());
+        // encode without creating a String
+        FastqEncoder.write(writer, rec);
+        // and print a new line
+        writer.println();
         if (writer.checkError()) {
             throw new SAMException("Error in writing fastq file " + path);
         }

src/main/java/htsjdk/samtools/fastq/FastqConstants.java

@@ -29,7 +29,9 @@
 public class FastqConstants {
     public static final String SEQUENCE_HEADER = "@" ;
     public static final String QUALITY_HEADER = "+" ;
-    
+    public static final String FIRST_OF_PAIR = "/1";
+    public static final String SECOND_OF_PAIR = "/2";
+
     public enum FastqExtensions {
         FASTQ(".fastq"),
         FASTQ_GZ(".fastq.gz"),

src/main/java/htsjdk/samtools/fastq/FastqEncoder.java

@@ -0,0 +1,113 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2016 Daniel Gomez-Sanchez
+ *
+ * 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 htsjdk.samtools.fastq;
+
+import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.util.SequenceUtil;
+
+import java.io.IOException;
+
+/**
+ * Codec for encoding records into FASTQ format.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+public final class FastqEncoder {
+
+    // cannot be instantiated because it is an utility class
+    private FastqEncoder() {}
+
+    /**
+     * Encodes a FastqRecord in the String FASTQ format.
+     */
+    public static String encode(final FastqRecord record) {
+        // reserve some memory based on the read length
+        int capacity = record.getReadLength() * 2 +  5;
+        // reserve some memory based on the read name
+        if (record.getReadName() != null) {
+            capacity += record.getReadName().length();
+        }
+        return write(new StringBuilder(capacity), record).toString();
+    }
+
+    /**
+     * Writes a FastqRecord into the Appendable output.
+     * @throws SAMException if any I/O error occurs.
+     */
+    public static Appendable write(final Appendable out,final FastqRecord record) {
+        final String readName = record.getReadName();
+        final String readString = record.getReadString();
+        final String qualHeader = record.getBaseQualityHeader();
+        final String qualityString = record.getBaseQualityString();
+        try {
+            return out.append(FastqConstants.SEQUENCE_HEADER)
+                    .append(readName == null ? "" : readName).append('\n')
+                    .append(readString == null ? "" : readString).append('\n')
+                    .append(FastqConstants.QUALITY_HEADER)
+                    .append(qualHeader == null ? "" : qualHeader).append('\n')
+                    .append(qualityString == null ? "" : qualityString);
+        } catch (IOException e) {
+            throw new SAMException(e);
+        }
+    }
+
+    /**
+     * Encodes a SAMRecord in the String FASTQ format.
+     * @see #encode(FastqRecord)
+     * @see #asSAMRecord(FastqRecord, SAMFileHeader)
+     */
+    public static String encode(final SAMRecord record) {
+        return encode(asFastqRecord(record));
+    }
+
+    /**
+     * Converts a {@link SAMRecord} into a {@link FastqRecord}.
+     */
+    public static FastqRecord asFastqRecord(final SAMRecord record) {
+        String readName = record.getReadName();
+        if(record.getReadPairedFlag() && (record.getFirstOfPairFlag() || record.getSecondOfPairFlag())) {
+            readName += (record.getFirstOfPairFlag()) ? FastqConstants.FIRST_OF_PAIR : FastqConstants.SECOND_OF_PAIR;
+        }
+        return new FastqRecord(readName, record.getReadString(), null, record.getBaseQualityString());
+    }
+
+    /**
+     * Converts a {@link FastqRecord} into a simple unmapped {@link SAMRecord}.
+     */
+    public static SAMRecord asSAMRecord(final FastqRecord record, final SAMFileHeader header) {
+        // construct the SAMRecord and set the unmapped flag
+        final SAMRecord samRecord = new SAMRecord(header);
+        samRecord.setReadUnmappedFlag(true);
+        // get the read name from the FastqRecord correctly formatted
+        final String readName = SequenceUtil.getSamReadNameFromFastqHeader(record.getReadName());
+        // set the basic information from the FastqRecord
+        samRecord.setReadName(readName);
+        samRecord.setReadBases(record.getReadBases());
+        samRecord.setBaseQualities(record.getBaseQualities());
+        return samRecord;
+    }
+
+}