/*
* 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 htsjdk.samtools.SAMFileReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Iterator;
/**
* Basic positive and negative tests for SplitSamByLibrary command-line program
*
* @author ktibbett@broadinstitute.org
*/
public class SplitSamByLibraryTest {
@Test
public void testNoLibrarySpecified() {
SplitSamByLibrary splitter = new SplitSamByLibrary();
splitter.INPUT = new File("testdata/picard/sam/invalid_coord_sort_order.sam");
Assert.assertEquals(splitter.doWork(), SplitSamByLibrary.NO_LIBRARIES_SPECIFIED_IN_HEADER,
"SAM file with no libraries should failed but didn't.");
}
@Test
public void basicPositiveTest() {
SplitSamByLibrary splitter = new SplitSamByLibrary();
splitter.INPUT = new File("testdata/picard/sam/split_test.sam");
Assert.assertEquals(splitter.doWork(), 0, "SAM file split should have succeeded but didn't.");
File f = new File("unknown.sam");
Assert.assertTrue(f.exists(), "uknown.sam should exist but doesn't");
Assert.assertEquals(countReads(f), 2, "unknown.sam has the wrong number of reads");
f.delete();
f = new File("lib-1.sam");
Assert.assertTrue(f.exists(), "lib-1.sam should exist but doesn't");
Assert.assertEquals(countReads(f), 6, "lib-1.sam has the wrong number of reads");
f.delete();
f = new File("lib-2.sam");
Assert.assertFalse(f.exists(), "lib-2.sam should not exist but does");
if (f.exists()) f.delete();
f = new File("lib-3.sam");
Assert.assertTrue(f.exists(), "lib-3.sam should exist but doesn't");
Assert.assertEquals(countReads(f), 2, "lib-3.sam has the wrong number of reads");
f.delete();
}
@Test
public void testNoUnknownFile() {
SplitSamByLibrary splitter = new SplitSamByLibrary();
splitter.INPUT = new File("testdata/picard/sam/split_test2.sam");
Assert.assertEquals(splitter.doWork(), 0, "SAM file split should have succeeded but didn't.");
// The unknown file should exist and have two reads
File f = new File("unknown.sam");
Assert.assertFalse(f.exists(), "uknown.sam should not exist but does");
if (f.exists()) f.delete();
f = new File("lib-1.sam");
Assert.assertTrue(f.exists(), "lib-1.sam should exist but doesn't");
Assert.assertEquals(countReads(f), 4, "lib-1.sam has the wrong number of reads");
f.delete();
f = new File("lib-3.sam");
Assert.assertTrue(f.exists(), "lib-3.sam should exist but doesn't");
Assert.assertEquals(countReads(f), 2, "lib-3.sam has the wrong number of reads");
f.delete();
}
private int countReads(File samFile) {
SAMFileReader reader = new SAMFileReader(samFile);
int count = 0;
for (Iterator it = reader.iterator(); it.hasNext();) {
it.next();
count++;
}
reader.close();
return count;
}
}