59 lines
2.3 KiB
Java
59 lines
2.3 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 edu.mit.broad.picard.illumina;
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import edu.mit.broad.picard.io.IoUtil;
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import java.io.File;
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/**
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* Given a Gerald directory, create a GeraldParser for one end or both ends as appropriate.
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*/
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public class GeraldParserFactory {
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// A Map of squashed reference chunk to reference genome sequence/chromosome. The chunk is represented as
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// a mapping (sequence=chunk file, startPos=offset into chunk file).
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private final SquashedCoordinateMap geraldToArachne;
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private final File geraldDir;
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private final int lane;
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public GeraldParserFactory(final File geraldDir, final int lane, final File squashedMapFile) {
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this.geraldDir = geraldDir;
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this.lane = lane;
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geraldToArachne = new SquashedCoordinateMap(squashedMapFile);
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}
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/** Attempts to determine if an analysis on a lane is PE or single. */
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public boolean isPairedRun() {
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if (new File(geraldDir, "s_" + lane + "_1_eland_query.txt").exists()) return true;
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else if (new File(geraldDir, "s_" + lane + "_eland_query.txt").exists()) return false;
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throw new IllegalStateException("Could not determine if gerald run is PE or fragment.");
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}
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private String makeLanePrefix(final Integer readNumber) {
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return "s_" + lane + "_" + (readNumber == null ? "" : readNumber + "_");
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}
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/**
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* @param readNumber 1 == first end of pair; 2 == second end of pair; null == unpaired
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* @return a GeraldParser for the given end
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*/
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public GeraldParser makeParser(final Integer readNumber) {
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final File elandExtendedFile = new File(geraldDir, makeLanePrefix(readNumber) + "eland_extended.txt");
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final File exportFile = new File(geraldDir, makeLanePrefix(readNumber) + "export.txt");
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IoUtil.assertFileIsReadable(elandExtendedFile);
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IoUtil.assertFileIsReadable(exportFile);
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return new GeraldParser(geraldToArachne, elandExtendedFile, exportFile);
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}
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}
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