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1 import java.io.IOException;
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2
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3 import _main.NGSrichEvaluate;
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4 import _main.NGSrichSummarize;
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5 import exceptions.FileFormatException;
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6
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7 /**
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8 * This is the main class.
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9 *
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10 * @author Peter Frommolt
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11 * @author Ali Abdallah
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12 */
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13
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14 public class NGSrich {
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15
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16 /**
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17 * Self Explanatory.
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18 *
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19 * @param args an Array of argument. The first argument is command and the
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20 * other arguments are its options.
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21 *
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22 * @throws FileFormatException if the used files have formally a bad format.
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23 * @throws IOException
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24 * @throws InterruptedException
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25 */
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26 public static void main(String[] args) throws FileFormatException,
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27 IOException, InterruptedException {
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28
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29 String usagestr =
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30 "\nThis is NGSrich, version 0.5.4.\n\n"
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31 + "Usage: java NGSrich [command] [options]\n\n"
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32 + "\tCommands:\n"
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33 + "\tevaluate"
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34 + "\tEvaluate target enrichment for a single sample.\n"
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35 + "\tsummarize"
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36 + "\tCreate a summary report for several evaluations.\n";
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37
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38 int alen = args.length;
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39 if (alen == 0) {
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40 System.out.println(usagestr);
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41 System.exit(0);
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42 } else {
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43 String[] cparams = new String[alen - 1];
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44 for (int i = 0; i < alen - 1; i = i + 1) {
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45 cparams[i] = args[i + 1];
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46 }
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47 String eval = "evaluate", summ = "summarize";
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48 if (eval.equals(args[0])) {
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49 // Geändert von AA 27.07.2011.
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50 new NGSrichEvaluate(cparams).evaluate();
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51 }
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52 if (summ.equals(args[0])) {
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53 // Geändert von AA 27.07.2011.
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54 new NGSrichSummarize(cparams).summarize();
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55 }
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56 }
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57 }
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58 } |
