/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.sam;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import picard.PicardException;
import java.io.File;
/**
* @author alecw@broadinstitute.org
*/
public class CreateSequenceDictionaryTest extends CommandLineProgramTest {
public static File TEST_DATA_DIR = new File("testdata/picard/sam");
public static File BASIC_FASTA = new File(TEST_DATA_DIR, "basic.fasta");
public static File DUPLICATE_FASTA = new File(TEST_DATA_DIR, "duplicate_sequence_names.fasta");
public String getCommandLineProgramName() {
return CreateSequenceDictionary.class.getSimpleName();
}
@Test
public void testBasic() throws Exception {
final File outputDict = File.createTempFile("CreateSequenceDictionaryTest.", ".dict");
outputDict.delete();
outputDict.deleteOnExit();
final String[] argv = {
"REFERENCE=" + BASIC_FASTA,
"OUTPUT=" + outputDict,
"TRUNCATE_NAMES_AT_WHITESPACE=false"
};
Assert.assertEquals(runPicardCommandLine(argv), 0);
}
/**
* Should throw an exception because with TRUNCATE_NAMES_AT_WHITESPACE, sequence names are not unique.
*/
@Test(expectedExceptions = PicardException.class)
public void testNonUniqueSequenceName() throws Exception {
final File outputDict = File.createTempFile("CreateSequenceDictionaryTest.", ".dict");
outputDict.deleteOnExit();
final String[] argv = {
"REFERENCE=" + DUPLICATE_FASTA,
"OUTPUT=" + outputDict,
"TRUNCATE_NAMES_AT_WHITESPACE=true"
};
Assert.assertEquals(runPicardCommandLine(argv), 0);
Assert.fail("Exception should have been thrown.");
}
}