Java tutorial
/** * Licensed to Big Data Genomics (BDG) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The BDG licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.bdgenomics.adam.io; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataInputStream; 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.CompressionCodecFactory; import org.apache.hadoop.mapreduce.InputSplit; import org.apache.hadoop.mapreduce.JobContext; import org.apache.hadoop.mapreduce.RecordReader; import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.input.FileSplit; import org.apache.hadoop.util.LineReader; import java.io.EOFException; import java.io.IOException; import java.io.InputStream; /** * This class is a Hadoop reader for single read fastq. * * This reader is based on the FastqInputFormat that's part of Hadoop-BAM, * found at https://github.com/HadoopGenomics/Hadoop-BAM/blob/master/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java * * @author Frank Austin Nothaft (fnothaft@berkeley.edu) * @date September 2014 */ public class SingleFastqInputFormat extends FileInputFormat<Void, Text> { public static class SingleFastqRecordReader extends RecordReader<Void, Text> { /* * fastq format: * <fastq> := <block>+ * <block> := @<seqname>\n<seq>\n\+[<seqname>]\n<qual>\n * <seqname> := [A-Za-z0-9_.:-]+ * <seq> := [A-Za-z\n\.~]+ * <qual> := [!-~\n]+ * * LP: this format is broken, no? You can have multi-line sequence and quality strings, * and the quality encoding includes '@' in its valid character range. So how should one * distinguish between \n@ as a record delimiter and and \n@ as part of a multi-line * quality string? * * For now I'm going to assume single-line sequences. This works for our sequencing * application. We'll see if someone complains in other applications. */ // start: first valid data index private long start; // end: first index value beyond the slice, i.e. slice is in range [start,end) private long end; // pos: current position in file private long pos; // file: the file being read private Path file; private LineReader lineReader; private InputStream inputStream; private Text currentValue; private byte[] newline = "\n".getBytes(); // How long can a read get? private static final int MAX_LINE_LENGTH = 10000; public SingleFastqRecordReader(Configuration conf, FileSplit split) throws IOException { file = split.getPath(); start = split.getStart(); end = start + split.getLength(); FileSystem fs = file.getFileSystem(conf); FSDataInputStream fileIn = fs.open(file); CompressionCodecFactory codecFactory = new CompressionCodecFactory(conf); CompressionCodec codec = codecFactory.getCodec(file); if (codec == null) { // no codec. Uncompressed file. positionAtFirstRecord(fileIn); inputStream = fileIn; } else { // compressed file if (start != 0) { throw new RuntimeException( "Start position for compressed file is not 0! (found " + start + ")"); } inputStream = codec.createInputStream(fileIn); end = Long.MAX_VALUE; // read until the end of the file } lineReader = new LineReader(inputStream); } /** * Position the input stream at the start of the first record. */ private void positionAtFirstRecord(FSDataInputStream stream) throws IOException { Text buffer = new Text(); if (true) { // (start > 0) // use start>0 to assume that files start with valid data // Advance to the start of the first record // We use a temporary LineReader to read lines until we find the // position of the right one. We then seek the file to that position. stream.seek(start); LineReader reader = new LineReader(stream); int bytesRead = 0; do { bytesRead = reader.readLine(buffer, (int) Math.min(MAX_LINE_LENGTH, end - start)); int bufferLength = buffer.getLength(); if (bytesRead > 0 && (bufferLength <= 0 || buffer.getBytes()[0] != '@')) { start += bytesRead; } else { // line starts with @. Read two more and verify that it starts with a + // // If this isn't the start of a record, we want to backtrack to its end long backtrackPosition = start + bytesRead; bytesRead = reader.readLine(buffer, (int) Math.min(MAX_LINE_LENGTH, end - start)); bytesRead = reader.readLine(buffer, (int) Math.min(MAX_LINE_LENGTH, end - start)); if (bytesRead > 0 && buffer.getLength() > 0 && buffer.getBytes()[0] == '+') { break; // all good! } else { // backtrack to the end of the record we thought was the start. start = backtrackPosition; stream.seek(start); reader = new LineReader(stream); } } } while (bytesRead > 0); stream.seek(start); } pos = start; } /** * Added to use mapreduce API. */ public void initialize(InputSplit split, TaskAttemptContext context) throws IOException, InterruptedException { } /** * Added to use mapreduce API. */ public Void getCurrentKey() { return null; } /** * Added to use mapreduce API. */ public Text getCurrentValue() { return currentValue; } /** * Added to use mapreduce API. */ public boolean nextKeyValue() throws IOException, InterruptedException { currentValue = new Text(); return next(currentValue); } /** * Close this RecordReader to future operations. */ public void close() throws IOException { inputStream.close(); } /** * Create an object of the appropriate type to be used as a key. */ public Text createKey() { return new Text(); } /** * Create an object of the appropriate type to be used as a value. */ public Text createValue() { return new Text(); } /** * Returns the current position in the input. */ public long getPos() { return pos; } /** * How much of the input has the RecordReader consumed i.e. */ public float getProgress() { if (start == end) return 1.0f; else return Math.min(1.0f, (pos - start) / (float) (end - start)); } public String makePositionMessage() { return file.toString() + ":" + pos; } protected boolean lowLevelFastqRead(Text readName, Text value) throws IOException { // ID line readName.clear(); long skipped = appendLineInto(readName, true); if (skipped == 0) return false; // EOF if (readName.getBytes()[0] != '@') throw new RuntimeException("unexpected fastq record didn't start with '@' at " + makePositionMessage() + ". Line: " + readName + ". \n"); value.append(readName.getBytes(), 0, readName.getLength()); // sequence appendLineInto(value, false); // separator line appendLineInto(value, false); // quality appendLineInto(value, false); return true; } /** * Reads the next key/value pair from the input for processing. */ public boolean next(Text value) throws IOException { if (pos >= end) return false; // past end of slice try { Text readName = new Text(); value.clear(); // first read of the pair boolean gotData = lowLevelFastqRead(readName, value); return gotData; } catch (EOFException e) { throw new RuntimeException("unexpected end of file in fastq record at " + makePositionMessage()); } } private int appendLineInto(Text dest, boolean eofOk) throws EOFException, IOException { Text buf = new Text(); int bytesRead = lineReader.readLine(buf, MAX_LINE_LENGTH); if (bytesRead < 0 || (bytesRead == 0 && !eofOk)) throw new EOFException(); dest.append(buf.getBytes(), 0, buf.getLength()); dest.append(newline, 0, 1); pos += bytesRead; return bytesRead; } } public RecordReader<Void, Text> createRecordReader(InputSplit genericSplit, TaskAttemptContext context) throws IOException, InterruptedException { context.setStatus(genericSplit.toString()); // cast as per example in TextInputFormat return new SingleFastqRecordReader(context.getConfiguration(), (FileSplit) genericSplit); } }