Package picard.illumina.parser

Source Code of picard.illumina.parser.MultiTileLocsParser

/*
* 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 picard.illumina.parser.readers.AbstractIlluminaPositionFileReader;
import picard.illumina.parser.readers.LocsFileReader;

import java.io.File;
import java.util.Collections;
import java.util.List;

/**
* Read locs file that contains multiple tiles in a single file.  A tile index is needed to parse this
* file so that {tile number, cluster number} can be converted into absolute record number in file.
*/
public class MultiTileLocsParser extends MultiTileParser<PositionalData> {
    private final LocsFileReader reader;
    private final int lane;

    public MultiTileLocsParser(final TileIndex tileIndex, final List<Integer> requestedTiles, final File locsFile, final int lane) {
        super(tileIndex, requestedTiles, Collections.singleton(IlluminaDataType.Position));
        final int tileNumber;
        if (requestedTiles.size() == 1) tileNumber = requestedTiles.get(0);
        else tileNumber = -1;
        this.reader = new LocsFileReader(locsFile, lane, tileNumber);
        this.lane = lane;
    }

    @Override
    PositionalData readNext() {
        final int tile = getTileOfNextCluster();
        final AbstractIlluminaPositionFileReader.PositionInfo nextVal = reader.next();
        return new PositionalData() {
            public int getXCoordinate() {
                return nextVal.xQseqCoord;
            }

            public int getYCoordinate() {
                return nextVal.yQseqCoord;
            }

            public int getLane() {
                return lane;
            }

            public int getTile() {
                return tile;
            }
        };
    }

    @Override
    void skipRecords(final int numToSkip) {
        reader.skipRecords(numToSkip);
    }

    @Override
    public void close() {
        reader.close();
    }
}
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