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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.
// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Hadoop-BAM.
//
// 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.seqdoop.hadoop_bam;
import java.io.DataOutputStream;
import java.io.OutputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat;
import org.apache.hadoop.util.ReflectionUtils;
import org.seqdoop.hadoop_bam.FormatConstants.BaseQualityEncoding;
/**
* Output format for Illumina qseq format.
* Records are lines of tab-separated fields. Each record consists of
* - Machine name
* - Run number
* - Lane number
* - Tile number
* - X coordinate of the spot. Integer (can be negative).
* - Y coordinate of the spot. Integer (can be negative).
* - Index
* - Read Number
* - Sequence
* - Quality
* - Filter
*/
public class QseqOutputFormat extends TextOutputFormat
{
public static final String CONF_BASE_QUALITY_ENCODING = "hbam.qseq-output.base-quality-encoding";
public static final String CONF_BASE_QUALITY_ENCODING_DEFAULT = "illumina";
public static class QseqRecordWriter extends RecordWriter
{
static final byte[] newLine;
static final String delim = "\t";
static {
try {
newLine = "\n".getBytes("us-ascii");
} catch (java.io.UnsupportedEncodingException e) {
throw new RuntimeException("us-ascii encoding not supported!");
}
}
protected StringBuilder sBuilder = new StringBuilder(800);
protected OutputStream out;
BaseQualityEncoding baseQualityFormat;
public QseqRecordWriter(Configuration conf, OutputStream out)
{
baseQualityFormat = BaseQualityEncoding.Illumina;
this.out = out;
setConf(conf);
}
public void setConf(Configuration conf)
{
String setting = conf.get(CONF_BASE_QUALITY_ENCODING, CONF_BASE_QUALITY_ENCODING_DEFAULT);
if ("illumina".equals(setting))
baseQualityFormat = BaseQualityEncoding.Illumina;
else if ("sanger".equals(setting))
baseQualityFormat = BaseQualityEncoding.Sanger;
else
throw new RuntimeException("Invalid property value '" + setting + "' for " + CONF_BASE_QUALITY_ENCODING + ". Valid values are 'illumina' or 'sanger'");
}
public void write(Text ignored_key, SequencedFragment seq) throws IOException
{
sBuilder.delete(0, sBuilder.length()); // clear
sBuilder.append( seq.getInstrument() == null ? "" : seq.getInstrument() ).append(delim);
sBuilder.append( seq.getRunNumber() == null ? "" : seq.getRunNumber().toString() ).append(delim);
sBuilder.append( seq.getLane() == null ? "" : seq.getLane().toString() ).append(delim);
sBuilder.append( seq.getTile() == null ? "" : seq.getTile().toString() ).append(delim);
sBuilder.append( seq.getXpos() == null ? "" : seq.getXpos().toString() ).append(delim);
sBuilder.append( seq.getYpos() == null ? "" : seq.getYpos().toString() ).append(delim);
String index;
if (seq.getIndexSequence() == null || seq.getIndexSequence().isEmpty())
index = "0";
else
index = seq.getIndexSequence().replace('N', '.');
sBuilder.append( index ).append(delim);
sBuilder.append( seq.getRead() == null ? "" : seq.getRead().toString() ).append(delim);
// here we also replace 'N' with '.'
sBuilder.append( seq.getSequence() == null ? "" : seq.getSequence().toString().replace('N', '.')).append(delim);
//////// quality may have to be re-coded
if (seq.getQuality() == null)
sBuilder.append("");
else
{
int startPos = sBuilder.length();
sBuilder.append(seq.getQuality().toString());
if (baseQualityFormat == BaseQualityEncoding.Sanger)
{
// do nothing
}
else if (baseQualityFormat == BaseQualityEncoding.Illumina)
{
// recode the quality in-place
for (int i = startPos; i < sBuilder.length(); ++i)
{
// cast to avoid warning about possible loss of precision for assigning a char from an int.
char newValue = (char)(sBuilder.charAt(i) + 31); // 64 - 33 = 31: difference between illumina and sanger encoding
if (newValue > 126)
throw new RuntimeException("output quality score over allowed range. Maybe you meant to write in Sanger format?");
sBuilder.setCharAt(i, newValue);
}
}
else
throw new RuntimeException("BUG! Unknown base quality format value " + baseQualityFormat + " in QseqRecordWriter");
}
sBuilder.append(delim);
/////////
sBuilder.append((seq.getFilterPassed() == null || seq.getFilterPassed() ) ? 1 : 0);
try {
ByteBuffer buf = Text.encode(sBuilder.toString());
out.write(buf.array(), 0, buf.limit());
} catch (java.nio.charset.CharacterCodingException e) {
throw new RuntimeException("Error encoding qseq record: " + seq);
}
out.write(newLine, 0, newLine.length);
}
public void close(TaskAttemptContext context) throws IOException
{
out.close();
}
}
public RecordWriter getRecordWriter(TaskAttemptContext task)
throws IOException
{
Configuration conf = task.getConfiguration();
boolean isCompressed = getCompressOutput(task);
CompressionCodec codec = null;
String extension = "";
if (isCompressed)
{
Class codecClass = getOutputCompressorClass(task, GzipCodec.class);
codec = (CompressionCodec) ReflectionUtils.newInstance(codecClass, conf);
extension = codec.getDefaultExtension();
}
Path file = getDefaultWorkFile(task, extension);
FileSystem fs = file.getFileSystem(conf);
OutputStream output;
if (isCompressed)
{
FSDataOutputStream fileOut = fs.create(file, false);
output = new DataOutputStream(codec.createOutputStream(fileOut));
}
else
output = fs.create(file, false);
return new QseqRecordWriter(conf, output);
}
}