66 lines
1.6 KiB
Java
66 lines
1.6 KiB
Java
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package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
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import java.lang.*;
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import java.util.*;
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import java.io.*;
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import org.broadinstitute.sting.utils.*;
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public class ConfusionMatrix
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{
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private double[][] ILLUMINA;
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private double[][] solid;
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private double[][] LS454;
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public ConfusionMatrix(String file_name)
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{
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//System.out.println("DBG: ConfusionMatrix constructor! (" + file_name + ")");
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ILLUMINA = new double[4][4];
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solid = new double[4][4];
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LS454 = new double[4][4];
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try
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{
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Scanner sc = new Scanner(new File(file_name));
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while (sc.hasNext())
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{
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String platform = sc.next();
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char read = sc.next().charAt(0);
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char ref = sc.next().charAt(0);
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double p = sc.nextDouble();
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int read_i = BaseUtils.simpleBaseToBaseIndex(read);
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int ref_i = BaseUtils.simpleBaseToBaseIndex(ref);
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if (platform.equals("ILLUMINA")) { ILLUMINA[read_i][ref_i] = p; }
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if (platform.equals("solid")) { solid[read_i][ref_i] = p; }
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if (platform.equals("LS454")) { LS454[read_i][ref_i] = p; }
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//System.out.println("DBG: " + key + " " + p);
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}
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}
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catch (Exception e)
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{
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e.printStackTrace();
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System.exit(-1);
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}
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}
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double lookup(String platform, char read, char truth)
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{
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int read_i = BaseUtils.simpleBaseToBaseIndex(read);
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int truth_i = BaseUtils.simpleBaseToBaseIndex(truth);
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double d = 0;
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if (platform.equals("ILLUMINA")) { d = ILLUMINA[read_i][truth_i]; }
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else if (platform.equals("solid")) { d = solid[read_i][truth_i]; }
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else if (platform.equals("LS454")) { d = LS454[read_i][truth_i]; }
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else { assert(false); }
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return d;
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}
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}
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