/*
* The MIT License
*
* Copyright (c) 2016 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.markduplicates;
import org.testng.annotations.Test;
/**
* This class defines the individual test cases to run. The actual running of the test is done
* by MarkDuplicatesWithMateCigarTester (see getTester).
* @author hogstrom@broadinstitute.org
*/
public class MarkDuplicatesTagRepresentativeReadIndexTest extends AbstractMarkDuplicatesCommandLineProgramTest {
protected MarkDuplicatesTagRepresentativeReadIndexTester getTester() {
return new MarkDuplicatesTagRepresentativeReadIndexTester();
}
// This tests the creation of a single duplicate pair. The expected size of the duplicate set is 2
// and the expected representative read is the first read defined in the text. The test fails if
// the 'DI' and 'DS' tags do not match the expectation.
@Test
public void testRepresentativeReadTag() {
final MarkDuplicatesTagRepresentativeReadIndexTester tester = getTester();
tester.testRepresentativeReads = true;
tester.setExpectedOpticalDuplicate(1);
String representativeReadName = "RUNID:1:1:16020:13352";
Integer representativeReadIndexInFileForward = 1;
tester.addMatePair(representativeReadName, 1, 485253, 485253, false, false, false, false, "45M", "45M", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(representativeReadIndexInFileForward, representativeReadIndexInFileForward);
tester.expectedRepresentativeIndexMap.put(3, representativeReadIndexInFileForward);
tester.expectedSetSizeMap.put(representativeReadName,2);
tester.addMatePair("RUNID:1:1:15993:13361", 1, 485253, 485253, false, false, true, true, "44M1S", "44M1S", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(0, representativeReadIndexInFileForward);
tester.expectedRepresentativeIndexMap.put(2, representativeReadIndexInFileForward);
tester.expectedSetSizeMap.put("RUNID:1:1:15993:13361",2);
tester.runTest();
}
// This tests the creation of a two duplicate sets of size 2 and 3 respectively. The test fails if
// the 'DI' and 'DS' tags do not match the expectation.
@Test
public void testMultiRepresentativeReadTags() {
final MarkDuplicatesTagRepresentativeReadIndexTester tester = getTester();
tester.testRepresentativeReads = true;
tester.setExpectedOpticalDuplicate(3);
// Duplicate set: size 2 - all optical
String representativeReadName1 = "RUNID:1:1:16020:13352";
Integer representativeReadIndexInFileForward = 1;
tester.addMatePair(representativeReadName1, 1, 485253, 485253, false, false, false, false, "45M", "45M", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(representativeReadIndexInFileForward, representativeReadIndexInFileForward);
tester.expectedRepresentativeIndexMap.put(3, representativeReadIndexInFileForward);
tester.expectedSetSizeMap.put(representativeReadName1,2);
tester.addMatePair("RUNID:1:1:15993:13361", 1, 485253, 485253, false, false, true, true, "44M1S", "44M1S", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(0, representativeReadIndexInFileForward);
tester.expectedRepresentativeIndexMap.put(2, representativeReadIndexInFileForward);
tester.expectedSetSizeMap.put("RUNID:1:1:15993:13361",2);
// Duplicate set: size 3 - all optical
String representativeReadName2 = "RUNID:1:1:15993:13360";
Integer representativeReadIndexInFileForward2 = 6;
tester.addMatePair(representativeReadName2, 1, 485299, 485299, false, false, false, false, "45M", "45M", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(representativeReadIndexInFileForward2, representativeReadIndexInFileForward2);
tester.expectedRepresentativeIndexMap.put(9, representativeReadIndexInFileForward2);
tester.expectedSetSizeMap.put(representativeReadName2,3);
tester.addMatePair("RUNID:1:1:15993:13365", 1, 485299, 485299, false, false, true, true, "44M1S", "44M1S", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(7, representativeReadIndexInFileForward2);
tester.expectedRepresentativeIndexMap.put(10, representativeReadIndexInFileForward2);
tester.expectedSetSizeMap.put("RUNID:1:1:15993:13365",3);
tester.addMatePair("RUNID:1:1:15993:13370", 1, 485299, 485299, false, false, true, true, "43M2S", "43M2S", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(8, representativeReadIndexInFileForward2);
tester.expectedRepresentativeIndexMap.put(11, representativeReadIndexInFileForward2);
tester.expectedSetSizeMap.put("RUNID:1:1:15993:13370",3);
// Add non-duplicate read
tester.addMatePair("RUNID:1:1:15993:13375", 1, 485255, 485255, false, false, false, false, "43M2S", "43M2S", false, true, false, false, false, DEFAULT_BASE_QUALITY);
tester.expectedRepresentativeIndexMap.put(4, null);
tester.expectedRepresentativeIndexMap.put(5, null);
tester.expectedSetSizeMap.put("RUNID:1:1:15993:13375",null);
tester.runTest();
}
}