/*
* The MIT License
*
* Copyright (c) 2014 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.DuplicateScoringStrategy.ScoringStrategy;
import picard.cmdline.CommandLineProgram;
/**
* This class is an extension of AbstractMarkDuplicatesCommandLineProgramTester used to test MarkDuplicatesWithMateCigar with SAM files generated on the fly.
* This performs the underlying tests defined by classes such as see AbstractMarkDuplicatesCommandLineProgramTest and MarkDuplicatesWithMateCigarTest.
*/
public class MarkDuplicatesWithMateCigarTester extends AbstractMarkDuplicatesCommandLineProgramTester {
public MarkDuplicatesWithMateCigarTester() {
// NB: to be equivalent to MarkDuplicates we need to use SUM_OF_BASE_QUALITIES
super(ScoringStrategy.TOTAL_MAPPED_REFERENCE_LENGTH);
addArg("MAX_RECORDS_IN_RAM=1000");
addArg("BLOCK_SIZE=250");
}
@Override
protected CommandLineProgram getProgram() { return new MarkDuplicatesWithMateCigar(); }
}