103 lines
3.5 KiB
Java
103 lines
3.5 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package org.broadinstitute.sting.secondarybase;
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import net.sf.picard.PicardException;
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import edu.mit.broad.picard.util.BasicTextFileParser;
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import net.sf.picard.util.FormatUtil;
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import java.io.File;
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/**
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* Class to parse the data in an Illumina Firecrest directory and return an iterator over that data, in order
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* by tile.
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*
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* @author Kiran Garimella
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*/
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public class FirecrestFileParser extends AbstractFirecrestFileParser {
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private BasicTextFileParser parser;
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private final FormatUtil formatter = new FormatUtil();
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private final File[] intensityFiles;
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/**
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* Constructor
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*
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* @param firecrestDirectory directory where the Firecrest files can be located
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* @param lane the lane to parse
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*/
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public FirecrestFileParser(final File firecrestDirectory, final int lane) {
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super(firecrestDirectory, lane);
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intensityFiles = getFilesMatchingRegexp("s_" + lane + "_\\d{4}_int.txt(.gz)?");
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}
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@Override
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public boolean isValidFirecrestDirectory() {
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return (intensityFiles.length > 0);
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}
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/**
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* Sorts the relevant files in the firecrestDirectory. Does some basic sanity checking to ensure that some files
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* are found and that they are the expected multiple for paired-end or not.
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*/
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@Override
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protected void prepareToIterate() {
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// Some basic sanity checking on file counts
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if (intensityFiles.length == 0) {
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throw new PicardException("No Firecrest 1.3 intensity files found in " + firecrestDirectory.getAbsolutePath() + " for lane " + lane);
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}
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// Sort each set of reads and create a text parser for it
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parser = makeParserForTextFiles(true, intensityFiles);
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}
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/**
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* Parses the next line from the parser and constructs a FirecrestReadData object from it
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* The first 4 fields are position information for the read, and the remaining value are
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* the intensities data.
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*
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* @return a fully populated FirecrestReadData object
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*/
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protected FirecrestReadData readNext() {
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if (!parser.hasNext()) {
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return null;
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}
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final String[] data = parser.next();
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final int lane = formatter.parseInt(data[0]);
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final int tile = formatter.parseInt(data[1]);
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final int x = formatter.parseInt(data[2]);
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final int y = formatter.parseInt(data[3]);
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int intensityOffset = 4;
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int numIntensities = (data.length - 4)/4;
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double[][] intensities = new double[numIntensities][4];
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for (int cycle = 0, index = intensityOffset; cycle < numIntensities; cycle++) {
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for (int channel = 0; channel < 4; channel++, index++) {
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intensities[cycle][channel] = formatter.parseFloat(data[index]);
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}
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}
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return new FirecrestReadData(lane, tile, x, y, intensities);
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}
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/**
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* Closes the underlying PasteParser
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*/
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@Override
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public void close() {
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if (parser != null) {
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parser.close();
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}
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}
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}
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