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1 package edu.unc.genomics;
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2
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3 import java.io.IOException;
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4 import java.nio.file.Files;
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5 import java.nio.file.Path;
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6 import java.nio.file.Paths;
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7 import java.util.zip.DataFormatException;
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8
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9 import com.beust.jcommander.IStringConverter;
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10 import com.beust.jcommander.ParameterException;
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11
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12 /**
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13 * @author timpalpant
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14 *
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15 */
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16 public class AssemblyConverter implements IStringConverter<Assembly> {
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17
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18 public static final Path ASSEMBLIES_DIR = Paths.get("resources", "assemblies");
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19
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20 @Override
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21 public Assembly convert(String value) throws ParameterException {
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22 // Look for the assembly in the resources/assemblies directory
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23 Path p = ASSEMBLIES_DIR.resolve(value+".len");
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24
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25 // If it does not exist in the assemblies directory, check if it is a path to a file
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26 if (!Files.isReadable(p)) {
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27 PathConverter converter = new PathConverter();
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28 p = converter.convert(value);
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29 // If it does not exist, then throw an exception that the assembly cannot be found
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30 if (!Files.isReadable(p)) {
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31 throw new ParameterException("Cannot find Assembly file: " + value);
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32 }
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33 }
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34
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35 // Attempt to load the assembly from file
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36 try {
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37 return new Assembly(p);
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38 } catch (IOException | DataFormatException e) {
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39 throw new ParameterException("Error loading Assembly from file: " + p);
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40 }
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41 }
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42
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43 }
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