/*
* The MIT License
*
* Copyright (c) 2014 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.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
public class SamFileConverterTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam/SamFileConverterTest");
private static final File unmappedSam = new File(TEST_DATA_DIR, "unmapped.sam");
private static final File unmappedBam = new File(TEST_DATA_DIR, "unmapped.bam");
private static final File unmappedCram = new File(TEST_DATA_DIR, "unmapped.cram");
@Test
public void testSAMToBAM() {
convertFile(unmappedSam, unmappedBam, ".bam");
}
@Test
public void testSAMToCRAM() {
convertFile(unmappedSam, unmappedCram, ".cram");
}
@Test
public void testBAMToCRAM() {
convertFile(unmappedBam, unmappedCram, ".cram");
}
@Test
public void testBAMToSAM() {
convertFile(unmappedBam, unmappedSam, ".sam");
}
@Test
public void testCRAMToBAM() {
convertFile(unmappedCram, unmappedBam, ".bam");
}
@Test
public void testCRAMToSAM() {
convertFile(unmappedCram, unmappedSam, ".sam");
}
private void convertFile(final File inputFile, final File fileToCompare, final String extension) {
final SamFormatConverter samFormatConverter = new SamFormatConverter();
final List<File> samFiles = new ArrayList<File>();
final ValidateSamFile validateSamFile = new ValidateSamFile();
final CompareSAMs compareSAMs = new CompareSAMs();
samFormatConverter.INPUT = inputFile;
try {
samFormatConverter.OUTPUT = File.createTempFile("SamFileConverterTest." + inputFile.getName(), extension);
samFormatConverter.OUTPUT.deleteOnExit();
} catch (final IOException e) {
e.printStackTrace();
}
samFormatConverter.doWork();
validateSamFile.INPUT = samFormatConverter.OUTPUT;
assertEquals(validateSamFile.doWork(), 0);
samFiles.add(samFormatConverter.OUTPUT);
samFiles.add(fileToCompare);
compareSAMs.samFiles = samFiles;
compareSAMs.doWork();
assertTrue(compareSAMs.areEqual());
}
}