/*
* 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 htsjdk.samtools;
import org.testng.Assert;
import org.testng.annotations.Test;
/**
* @author alecw@broadinstitute.org
*/
public class SAMCloneTest {
private SAMRecordSetBuilder getSAMReader(final boolean sortForMe, final SAMFileHeader.SortOrder sortOrder) {
final SAMRecordSetBuilder ret = new SAMRecordSetBuilder(sortForMe, sortOrder);
ret.addPair("readB", 20, 200, 300);
ret.addPair("readA", 20, 100, 150);
ret.addFrag("readC", 20, 140, true);
ret.addFrag("readD", 20, 140, false);
return ret;
}
@Test
public void testBasic() throws Exception {
final SAMRecordSetBuilder recordSetBuilder = getSAMReader(true, SAMFileHeader.SortOrder.coordinate);
SAMFileReader inputSAM = recordSetBuilder.getSamReader();
for (final SAMRecord samRecord : inputSAM) {
SAMRecord newRecord = (SAMRecord)samRecord.clone();
Assert.assertEquals(newRecord, samRecord);
}
inputSAM.close();
}
}