/*
* 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.readers;
import htsjdk.samtools.util.CloserUtil;
import picard.PicardException;
import picard.util.BasicInputParser;
import java.io.File;
/**
* The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
* pos files store position data for successive clusters in tabbed delimited coordinated pairs, 1 per file row e.g.:
*
* xPos1\tyPos1
* xPos2\tyPos2
* 102.0\t303.3
* ...
* xPosn-1\yPosn-1
* xPosn\yPosn
*
* Where n = the total number of clusters (and therefore lines) in the file.
*/
public class PosFileReader extends AbstractIlluminaPositionFileReader {
private final BasicInputParser parser;
public PosFileReader(final File posFile) {
super(posFile);
this.parser = new BasicInputParser(true, posFile);
}
/** Read a line of text and parse it into two float values, create a PositionInfo and return it */
@Override
protected PositionInfo unsafeNextInfo() {
final String [] strVals = this.parser.next();
if(strVals.length != 2) {
throw new PicardException("Pos file number of values != 2, found (" + strVals.length +")" + makeExceptionMsg());
}
try {
final float xVal = Float.parseFloat(strVals[0]);
final float yVal = Float.parseFloat(strVals[1]);
if(xVal <0 || yVal < 0) {
throw new NumberFormatException("X and Y pos values cannot be negative!");
}
return new PositionInfo(xVal, yVal, getLane(), getTile());
} catch(final NumberFormatException nfe) {
throw new PicardException("Bad x or y value in " + makeExceptionMsg(), nfe);
}
}
@Override
protected String makeExceptionMsg() {
return "pos file( " + parser.getFileName() +
" ) on line number( " + parser.getCurrentLineNumber() +
" ) with current line = " + parser.getCurrentLine();
}
public boolean hasNext() {
return parser.hasNext();
}
public void close() {
CloserUtil.close(parser);
}
}