/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF 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 fr.ens.biologie.genomique.eoulsan.bio.io.hadoop;
import java.io.IOException;
import java.io.InputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.SplitCompressionInputStream;
import org.apache.hadoop.mapreduce.lib.input.SplitLineReader;
public class CompressedSplitFastqLineReader extends SplitLineReader {
SplitCompressionInputStream scin;
private boolean usingCRLF;
private boolean needAdditionalRecord = false;
private boolean finished = false;
private boolean cont = false;
public CompressedSplitFastqLineReader(SplitCompressionInputStream in,
Configuration conf, byte[] recordDelimiterBytes) throws IOException {
super(in, conf, recordDelimiterBytes);
scin = in;
usingCRLF = (recordDelimiterBytes == null);
}
@Override
protected int fillBuffer(InputStream in, byte[] buffer, boolean inDelimiter)
throws IOException {
int bytesRead = in.read(buffer);
// If the split ended in the middle of a record delimiter then we need
// to read one additional record, as the consumer of the next split will
// not recognize the partial delimiter as a record.
// However if using the default delimiter and the next character is a
// linefeed then next split will treat it as a delimiter all by itself
// and the additional record read should not be performed.
if (inDelimiter && bytesRead > 0) {
if (usingCRLF) {
needAdditionalRecord = (buffer[0] != '\n');
} else {
needAdditionalRecord = true;
}
}
return bytesRead;
}
@Override
public int readLine(Text str, int maxLineLength, int maxBytesToConsume)
throws IOException {
int bytesRead = 0;
if (!finished) {
// only allow at most one more record to be read after the stream
// reports the split ended
if (scin.getPos() > scin.getAdjustedEnd() && !this.cont) {
finished = true;
}
bytesRead = super.readLine(str, maxLineLength, maxBytesToConsume);
}
return bytesRead;
}
@Override
public boolean needAdditionalRecordAfterSplit() {
return !finished && needAdditionalRecord;
}
void setContinue(final boolean cont) {
this.cont = cont;
}
}