/*
* The MIT License
*
* Copyright (c) 2012 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.PicardException;
import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader;
import picard.illumina.parser.readers.ClocsFileReader;
import picard.illumina.parser.readers.LocsFileReader;
import picard.illumina.parser.readers.PosFileReader;
import java.io.File;
import java.util.Collections;
import java.util.Set;
import static htsjdk.samtools.util.CollectionUtil.makeSet;
/**
* PosParser parses multiple files formatted as one of the three file formats that contain position information
* only (pos, locs, and clocs). This parser takes a map from tilesToFiles and a FileType enum value indicating
* whether or not these are POS,LOCS, or CLOCS files. The only client classes to this class should be IlluminaDataProvider
* and test classes. Check out AbstractIlluminaFileReader, PosFileReader, LocsFileReader, and ClocsFileReader for
* more information on Position related illumina files.
*/
public class PosParser extends PerTileParser<PositionalData> {
private static Set<IlluminaDataType> supportedTypes = Collections.unmodifiableSet(makeSet(IlluminaDataType.Position));
/** The FileType of the files we are parsing */
private final IlluminaFileUtil.SupportedIlluminaFormat fileType;
public PosParser(final IlluminaFileMap tilesToFiles, final IlluminaFileUtil.SupportedIlluminaFormat fileType) {
super(tilesToFiles);
this.fileType = fileType;
}
public PosParser(final IlluminaFileMap tilesToFiles, final int startingTile, final IlluminaFileUtil.SupportedIlluminaFormat fileType) {
super(tilesToFiles, startingTile);
this.fileType = fileType;
}
/**
* Make an CloseableIterator<PositionalData> based on the given file and fileType specified at construction.
* This method wraps a reader in an iterator that converts it's output to the output format expected by
* IlluminaDataProvider (PositionalData).
* @param file A file for the current tile being parsed
* @return An iterator over the PositionalData in that file.
*/
@Override
protected CloseableIterator<PositionalData> makeTileIterator(final File file) {
final AbstractIlluminaPositionFileReader fileReader;
switch(fileType){
case Pos:
fileReader = new PosFileReader(file);
break;
case Locs:
fileReader = new LocsFileReader(file);
break;
case Clocs:
fileReader = new ClocsFileReader(file);
break;
default:
throw new PicardException("Unrecognized pos file type " + fileType.name());
}
return new CloseableIterator<PositionalData>() {
private AbstractIlluminaPositionFileReader reader = fileReader;
public void close() {
reader.close();
}
public boolean hasNext() {
return reader.hasNext();
}
public PositionalData next() {
final AbstractIlluminaPositionFileReader.PositionInfo nextValue = reader.next();
return new PositionalData() {
public int getXCoordinate() {
return nextValue.xQseqCoord;
}
public int getYCoordinate() {
return nextValue.yQseqCoord;
}
public int getLane() {
return nextValue.lane;
}
public int getTile() {
return nextValue.tile;
}
};
}
public void remove() {
throw new UnsupportedOperationException();
}
};
}
@Override
public Set<IlluminaDataType> supportedTypes() {
return supportedTypes;
}
}