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 brush; import java.io.EOFException; import java.io.IOException; import java.io.InputStream; 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.RecordReader; import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.apache.hadoop.mapreduce.lib.input.FileSplit; import org.apache.hadoop.util.LineReader; /** * A record reader for the interleaved FASTQ format. * * Reads over an input file and parses interleaved FASTQ read pairs into * a single Text output. This is then fed into the FastqConverter, which * converts the single Text instance into two AlignmentRecords. */ abstract class FastqRecordReader 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. */ /** * First valid data index in the stream. */ private long start; /** * First index value beyond the slice, i.e. slice is in range [start,end). */ protected long end; /** * Current position in file. */ protected long pos; /** * Path of the file being parsed. */ private Path file; /** * The line reader we are using to read the file. */ private LineReader lineReader; /** * The input stream we are using to read the file. */ private InputStream inputStream; /** * The text for a single record pair we have parsed out. * Hadoop's RecordReader contract requires us to save this as state. */ private Text currentValue; /** * Newline string for matching on. */ private static final byte[] newline = "\n".getBytes(); /** * Maximum length for a read string. */ private static final int MAX_LINE_LENGTH = 10000; /** * Builds a new record reader given a config file and an input split. * * @param conf The Hadoop configuration object. Used for gaining access * to the underlying file system. * @param split The file split to read. */ protected FastqRecordReader(final Configuration conf, final 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); } /** * Checks to see whether the buffer is positioned at a valid record. * * @param bufferLength The length of the line currently in the buffer. * @param buffer A buffer containing a peek at the first line in the current * stream. * @return Returns true if the buffer contains the first line of a properly * formatted FASTQ record. */ abstract protected boolean checkBuffer(int bufferLength, Text buffer); /** * Position the input stream at the start of the first record. * * @param stream The stream to reposition. */ protected 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 that ends with /1 // 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 && !checkBuffer(bufferLength, buffer)) { 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; } /** * Method is a no-op. * * @param split The input split that we will parse. * @param context The Hadoop task context. */ public void initialize(InputSplit split, TaskAttemptContext context) throws IOException, InterruptedException { } /** * FASTQ has no keys, so we return null. * * @return Always returns null. */ public Void getCurrentKey() { return null; } /** * Returns the last interleaved FASTQ record. * * @return The text corresponding to the last read pair. */ public Text getCurrentValue() { return currentValue; } /** * Seeks ahead in our split to the next key-value pair. * * Triggers the read of an interleaved FASTQ read pair, and populates * internal state. * * @return True if reading the next read pair succeeded. */ 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(); } /** * How much of the input has the RecordReader consumed? * * @return Returns a value on [0.0, 1.0] that notes how many bytes we * have read so far out of the total bytes to read. */ public float getProgress() { if (start == end) { return 1.0f; } else { return Math.min(1.0f, (pos - start) / (float) (end - start)); } } /** * Produces a debugging message with the file position. * * @return Returns a string containing {filename}:{index}. */ protected String makePositionMessage() { return file.toString() + ":" + pos; } /** * Parses a read from an interleaved FASTQ file. * * Only reads a single record. * * @param readName Text record containing read name. Output parameter. * @param value Text record containing full record. Output parameter. * @return Returns true if read was successful (did not hit EOF). * * @throws RuntimeException Throws exception if FASTQ record doesn't * have proper formatting (e.g., record doesn't start with @). */ protected boolean lowLevelFastqRead(Text readName, Text value) throws IOException { // ID line readName.clear(); long skipped = appendLineInto(readName, true); pos += skipped; 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 from the input split. * * @param value Text record to write input value into. * @return Returns whether this read was successful or not. * * //@see lowLevelFastqRead */ abstract protected boolean next(Text value) throws IOException; /** * Reads a newline into a text record from the underlying line reader. * * @param dest Text record to read line into. * @param eofOk Whether an EOF is acceptable in this line. * @return Returns the number of bytes read. * * @throws EOFException Throws if eofOk was false and we hit an EOF in * the current line. */ private int appendLineInto(final Text dest, final 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; } }