79 lines
2.9 KiB
Java
79 lines
2.9 KiB
Java
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/*
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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 java.io.File;
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import java.util.Comparator;
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/**
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* Comparator for getting Bustard files in "sorted" order for use by the BustardFileParser. Expected order is
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* by lane in ascending order, then by tile in ascending order, then:
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* the read 1 qseq file
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* the read 2 qseq file
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* the sig2 file
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*
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* IMPORTANT: Currently this class expects to receive ONLY qseq and sig2 files.
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*
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* @author Kathleen Tibbetts
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*/
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public class BustardFilenameComparator implements Comparator<File> {
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/**
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* Compares its two arguments for order. Returns a negative integer, zero, or a positive integer as
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* the first argument is less than, equal to, or greater than the second.
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*
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* @param file1
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* @param file2
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* @return a negative integer, zero, or a positive integer as
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* the first argument is less than, equal to, or greater than the second.
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*/
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public int compare(File file1, File file2)
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{
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Integer parts1[] = parseFileNameParts(file1.getName());
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Integer parts2[] = parseFileNameParts(file2.getName());
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for (int i = 1; i < parts1.length; i++)
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{
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if (!parts1[i].equals(parts2[i])) {
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return parts1[i].compareTo(parts2[i]);
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}
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}
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return 0;
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}
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/**
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* Utility method that returns an array of integers that represent, in order,
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* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
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* represented by the given file name
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*
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* @param name
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* @return an array of integers that represent, in order,
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* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
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* represented by the given file name
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*/
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private Integer[] parseFileNameParts(String name)
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{
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Integer parts[] = new Integer[4]; // Lane, tile, type, read
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String src[] = name.split("_");
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parts[0] = new Integer(src[1]); // Lane is always the second part
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if (src[2].length() == 4) { // Tile is 3rd or fourth
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parts[1] = new Integer(src[2]);
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}
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else {
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parts[1] = new Integer(src[3]);
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}
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parts[2] = (src[src.length-1].equals("qseq.txt")) ? 0 : 1; // qseq tests are lower
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if (src[2].length() == 1) { // read is last
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parts[3] = new Integer(src[2]);
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}
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return parts;
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}
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}
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