/*
* 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 htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloserUtil;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
/**
* Tests a few hand build sam files as they are.
*/
public class AsIsMarkDuplicatesTester {
@DataProvider
public Object[][] testSameUnclipped5PrimeOppositeStrandData() {
final File TEST_DIR = new File("testdata/picard/sam/MarkDuplicates");
return new Object[][]{
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndv1.sam")},
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndv2.sam")},
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndCoordinateSortedv1.sam")},
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndCoordinateSortedv2.sam")},
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndCoordinateSortedv3.sam")},
new Object[]{new File(TEST_DIR, "sameUnclipped5primeEndCoordinateSortedv4.sam")}
};
}
@Test(dataProvider = "testSameUnclipped5PrimeOppositeStrandData")
public void testSameUnclipped5PrimeOppositeStrand(final File input) {
final AbstractMarkDuplicatesCommandLineProgramTester tester = new BySumOfBaseQAndInOriginalOrderMDTester();
final SamReader reader = SamReaderFactory.makeDefault().open(input);
tester.setHeader(reader.getFileHeader());
reader.iterator().stream().forEach(tester::addRecord);
CloserUtil.close(reader);
tester.setExpectedOpticalDuplicate(0);
tester.runTest();
}
}