/*
* The MIT License
*
* Copyright (c) 2011 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 htsjdk.samtools.BamFileIoUtils;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import picard.sam.testers.ValidateSamTester;
import java.io.File;
public class MergeSamFilesTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam/MergeSamFiles");
public String getCommandLineProgramName() {
return MergeSamFiles.class.getSimpleName();
}
/**
* Confirm that unsorted input can result in coordinate sorted output, with index created.
*/
@Test
public void unsortedInputSortedOutputTest() throws Exception {
final File unsortedInputTestDataDir = new File(TEST_DATA_DIR, "unsorted_input");
final File mergedOutput = File.createTempFile("unsortedInputSortedOutputTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
mergedOutput.deleteOnExit();
final String[] args = {
"I=" + new File(unsortedInputTestDataDir, "1.sam").getAbsolutePath(),
"I=" + new File(unsortedInputTestDataDir, "2.sam").getAbsolutePath(),
"O=" + mergedOutput.getAbsolutePath(),
"SO=coordinate"
};
final int mergeExitStatus = runPicardCommandLine(args);
Assert.assertEquals(mergeExitStatus, 0);
final SAMFileReader reader = new SAMFileReader(mergedOutput);
Assert.assertEquals(reader.getFileHeader().getSortOrder(), SAMFileHeader.SortOrder.coordinate);
new ValidateSamTester().assertSamValid(mergedOutput);
}
}