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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.IOException;
import java.io.InputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
/**
* A class that provides a line reader from an input stream.
* This code started as the org.apache.hadoop.util.LineReader class in Hadoop 0.20.2,
* to which we added a skip(n) method.
*/
public class LineReader {
private static final int DEFAULT_BUFFER_SIZE = 64 * 1024;
private int bufferSize = DEFAULT_BUFFER_SIZE;
private InputStream in;
private byte[] buffer;
// the number of bytes of real data in the buffer
private int bufferLength = 0;
// the current position in the buffer
private int bufferPosn = 0;
private static final byte CR = '\r';
private static final byte LF = '\n';
/**
* Create a line reader that reads from the given stream using the
* default buffer-size (64k).
* @param in The input stream
* @throws IOException
*/
public LineReader(InputStream in) {
this(in, DEFAULT_BUFFER_SIZE);
}
/**
* Create a line reader that reads from the given stream using the
* given buffer-size.
* @param in The input stream
* @param bufferSize Size of the read buffer
* @throws IOException
*/
public LineReader(InputStream in, int bufferSize) {
this.in = in;
this.bufferSize = bufferSize;
this.buffer = new byte[this.bufferSize];
}
/**
* Create a line reader that reads from the given stream using the
* io.file.buffer.size specified in the given
* Configuration.
* @param in input stream
* @param conf configuration
* @throws IOException
*/
public LineReader(InputStream in, Configuration conf) throws IOException {
this(in, conf.getInt("io.file.buffer.size", DEFAULT_BUFFER_SIZE));
}
/**
* Close the underlying stream.
* @throws IOException
*/
public void close() throws IOException {
in.close();
}
/**
* Read one line from the InputStream into the given Text. A line
* can be terminated by one of the following: '\n' (LF) , '\r' (CR),
* or '\r\n' (CR+LF). EOF also terminates an otherwise unterminated
* line.
*
* @param str the object to store the given line (without newline)
* @param maxLineLength the maximum number of bytes to store into str;
* the rest of the line is silently discarded.
* @param maxBytesToConsume the maximum number of bytes to consume
* in this call. This is only a hint, because if the line cross
* this threshold, we allow it to happen. It can overshoot
* potentially by as much as one buffer length.
*
* @return the number of bytes read including the (longest) newline
* found.
*
* @throws IOException if the underlying stream throws
*/
public int readLine(Text str, int maxLineLength,
int maxBytesToConsume) throws IOException {
/* We're reading data from in, but the head of the stream may be
* already buffered in buffer, so we have several cases:
* 1. No newline characters are in the buffer, so we need to copy
* everything and read another buffer from the stream.
* 2. An unambiguously terminated line is in buffer, so we just
* copy to str.
* 3. Ambiguously terminated line is in buffer, i.e. buffer ends
* in CR. In this case we copy everything up to CR to str, but
* we also need to see what follows CR: if it's LF, then we
* need consume LF as well, so next call to readLine will read
* from after that.
* We use a flag prevCharCR to signal if previous character was CR
* and, if it happens to be at the end of the buffer, delay
* consuming it until we have a chance to look at the char that
* follows.
*/
str.clear();
int txtLength = 0; //tracks str.getLength(), as an optimization
int newlineLength = 0; //length of terminating newline
boolean prevCharCR = false; //true of prev char was CR
long bytesConsumed = 0;
do {
int startPosn = bufferPosn; //starting from where we left off the last time
if (bufferPosn >= bufferLength) {
startPosn = bufferPosn = 0;
if (prevCharCR)
++bytesConsumed; //account for CR from previous read
bufferLength = in.read(buffer);
if (bufferLength <= 0)
break; // EOF
}
for (; bufferPosn < bufferLength; ++bufferPosn) { //search for newline
if (buffer[bufferPosn] == LF) {
newlineLength = (prevCharCR) ? 2 : 1;
++bufferPosn; // at next invocation proceed from following byte
break;
}
if (prevCharCR) { //CR + notLF, we are at notLF
newlineLength = 1;
break;
}
prevCharCR = (buffer[bufferPosn] == CR);
}
int readLength = bufferPosn - startPosn;
if (prevCharCR && newlineLength == 0)
--readLength; //CR at the end of the buffer
bytesConsumed += readLength;
int appendLength = readLength - newlineLength;
if (appendLength > maxLineLength - txtLength) {
appendLength = maxLineLength - txtLength;
}
if (appendLength > 0) {
str.append(buffer, startPosn, appendLength);
txtLength += appendLength;
}
} while (newlineLength == 0 && bytesConsumed < maxBytesToConsume);
if (bytesConsumed > (long)Integer.MAX_VALUE)
throw new IOException("Too many bytes before newline: " + bytesConsumed);
return (int)bytesConsumed;
}
/**
* Read from the InputStream into the given Text.
* @param str the object to store the given line
* @param maxLineLength the maximum number of bytes to store into str.
* @return the number of bytes read including the newline
* @throws IOException if the underlying stream throws
*/
public int readLine(Text str, int maxLineLength) throws IOException {
return readLine(str, maxLineLength, Integer.MAX_VALUE);
}
/**
* Read from the InputStream into the given Text.
* @param str the object to store the given line
* @return the number of bytes read including the newline
* @throws IOException if the underlying stream throws
*/
public int readLine(Text str) throws IOException {
return readLine(str, Integer.MAX_VALUE, Integer.MAX_VALUE);
}
/**
* Skip n bytes from the InputStream.
* @param n the number of bytes to skip.
* @return the number of bytes skipped.
* @throws IOException if the underlying stream throws.
*/
public long skip(long n) throws IOException
{
boolean end = false;
long toskip = n;
while (toskip > 0 && !end)
{
if (bufferPosn < bufferLength)
{
int skipped = (int)Math.min(bufferLength - bufferPosn, toskip);
bufferPosn += skipped;
toskip -= skipped;
}
if (bufferPosn >= bufferLength)
{
int loaded = loadBuffer();
end = loaded == 0;
}
}
return n - toskip;
}
protected int loadBuffer() throws IOException
{
bufferLength = in.read(buffer);
if (bufferLength < 0) // if EOF read returns -1
bufferLength = 0;
bufferPosn = 0;
return bufferLength;
}
}