/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* 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 picard.illumina.parser;
import htsjdk.samtools.util.CloseableIterator;
import picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import picard.illumina.parser.readers.BclReader;
import java.io.File;
import java.util.List;
import java.util.NoSuchElementException;
/**
* Parse .bcl.bgzf files that contain multiple tiles in a single file. This requires an index file that tells
* the bgzf virtual file offset of the start of each tile in the block-compressed bcl file.
*/
public class MultiTileBclParser extends BclParser {
private final TileIndex tileIndex;
private MultiTileBclDataCycleFileParser cycleFileParser = null;
public MultiTileBclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles,
final OutputMapping outputMapping, final boolean applyEamssFilter,
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
final TileIndex tileIndex) {
super(directory, lane, tilesToCycleFiles, outputMapping, applyEamssFilter, bclQualityEvaluationStrategy);
this.tileIndex = tileIndex;
this.initialize();
}
@Override
public void initialize(){
if(tileIndex != null){
seekToTile(currentTile);
}
}
private CountLimitedIterator makeReader(final List<File> files) {
if(tileIndex != null) {
final BclReader bclReader = BclReader.makeSeekable(files, bclQualityEvaluationStrategy, outputMapping.getOutputReadLengths());
final int numClustersInTile = bclReader.seek(files, tileIndex, currentTile);
return new CountLimitedIterator(bclReader, numClustersInTile);
}
else{
return null;
}
}
@Override
protected CycleFilesParser<BclData> makeCycleFileParser(final List<File> files) {
if (cycleFileParser == null) {
cycleFileParser = new MultiTileBclDataCycleFileParser(files, currentTile);
} else {
final int numClustersInTile = cycleFileParser.getReader().seek(files, tileIndex, currentTile);
cycleFileParser.setCurrentTile(currentTile);
cycleFileParser.resetClusterLimit(numClustersInTile);
}
return cycleFileParser;
}
/**
* An iterator wrapper that stops when it has return a pre-determined number of records even if the underlying
* iterator still had more records.
*/
static class CountLimitedIterator implements CloseableIterator<BclData> {
public BclReader getUnderlyingIterator() {
return underlyingIterator;
}
private final BclReader underlyingIterator;
private int recordLimit;
private int numRecordsRead = 0;
CountLimitedIterator(final BclReader underlyingIterator, final int recordLimit) {
this.underlyingIterator = underlyingIterator;
this.recordLimit = recordLimit;
}
@Override
public void close() {
//underlyingIterator.close();
}
@Override
public boolean hasNext() {
return numRecordsRead < recordLimit && underlyingIterator.hasNext();
}
@Override
public BclData next() {
if (!hasNext()) throw new NoSuchElementException();
++numRecordsRead;
return underlyingIterator.next();
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
}
private class MultiTileBclDataCycleFileParser implements CycleFilesParser<BclData> {
final CountLimitedIterator reader;
int currentTile;
public MultiTileBclDataCycleFileParser(final List<File> files, final int currentTile) {
this.currentTile = currentTile;
reader = makeReader(files);
}
@Override
public void close() {
reader.close();
}
@Override
public BclData next() {
if (!hasNext()) {
throw new NoSuchElementException();
}
return reader.next();
}
@Override
public boolean hasNext() {
try {
return reader.hasNext();
} catch (final NullPointerException npe) {
return false;
}
}
public int getCurrentTile(){
return currentTile;
}
public BclReader getReader() {
return reader.getUnderlyingIterator();
}
public void resetClusterLimit(final int numClustersInTile) {
reader.recordLimit = numClustersInTile;
reader.numRecordsRead = 0;
}
public void setCurrentTile(final int currentTile) {
this.currentTile = currentTile;
}
}
}