59 lines
2.3 KiB
Java
59 lines
2.3 KiB
Java
|
/*
|
||
|
|
* The Broad Institute
|
||
|
|
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
||
|
|
* This software and its documentation are copyright 2009 by the
|
||
|
|
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
||
|
|
*
|
||
|
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
||
|
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
||
|
|
*/
|
||
|
|
package edu.mit.broad.picard.illumina;
|
||
|
|
|
||
|
|
import edu.mit.broad.picard.io.IoUtil;
|
||
|
|
|
||
|
|
import java.io.File;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Given a Gerald directory, create a GeraldParser for one end or both ends as appropriate.
|
||
|
|
*/
|
||
|
|
public class GeraldParserFactory {
|
||
|
|
|
||
|
|
// A Map of squashed reference chunk to reference genome sequence/chromosome. The chunk is represented as
|
||
|
|
// a mapping (sequence=chunk file, startPos=offset into chunk file).
|
||
|
|
private final SquashedCoordinateMap geraldToArachne;
|
||
|
|
private final File geraldDir;
|
||
|
|
private final int lane;
|
||
|
|
|
||
|
|
public GeraldParserFactory(final File geraldDir, final int lane, final File squashedMapFile) {
|
||
|
|
this.geraldDir = geraldDir;
|
||
|
|
this.lane = lane;
|
||
|
|
geraldToArachne = new SquashedCoordinateMap(squashedMapFile);
|
||
|
|
}
|
||
|
|
|
||
|
|
/** Attempts to determine if an analysis on a lane is PE or single. */
|
||
|
|
public boolean isPairedRun() {
|
||
|
|
if (new File(geraldDir, "s_" + lane + "_1_eland_query.txt").exists()) return true;
|
||
|
|
else if (new File(geraldDir, "s_" + lane + "_eland_query.txt").exists()) return false;
|
||
|
|
|
||
|
|
throw new IllegalStateException("Could not determine if gerald run is PE or fragment.");
|
||
|
|
}
|
||
|
|
|
||
|
|
private String makeLanePrefix(final Integer readNumber) {
|
||
|
|
return "s_" + lane + "_" + (readNumber == null ? "" : readNumber + "_");
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* @param readNumber 1 == first end of pair; 2 == second end of pair; null == unpaired
|
||
|
|
* @return a GeraldParser for the given end
|
||
|
|
*/
|
||
|
|
public GeraldParser makeParser(final Integer readNumber) {
|
||
|
|
final File elandExtendedFile = new File(geraldDir, makeLanePrefix(readNumber) + "eland_extended.txt");
|
||
|
|
final File exportFile = new File(geraldDir, makeLanePrefix(readNumber) + "export.txt");
|
||
|
|
IoUtil.assertFileIsReadable(elandExtendedFile);
|
||
|
|
IoUtil.assertFileIsReadable(exportFile);
|
||
|
|
return new GeraldParser(geraldToArachne, elandExtendedFile, exportFile);
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|