CollectQualityYieldMetricsTest.java

/*
 * The MIT License
 *
 * Copyright (c) 2015 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.analysis;

import htsjdk.samtools.metrics.MetricsFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;

import java.io.File;
import java.io.FileReader;
import java.io.IOException;

/**
 * Created by kbergin on 11/23/15.
 */
public class CollectQualityYieldMetricsTest extends CommandLineProgramTest {
    private static final File TEST_DATA_DIR = new File("testdata/picard/sam/");

    public String getCommandLineProgramName() {
        return CollectQualityYieldMetrics.class.getSimpleName();
    }

    @Test
    public void test() throws IOException {
        final File input = new File(TEST_DATA_DIR, "insert_size_metrics_test.sam");
        final File outfile   = File.createTempFile("test", ".quality_yield_metrics");
        outfile.deleteOnExit();
        final String[] args = new String[] {
                "INPUT="  + input.getAbsolutePath(),
                "OUTPUT=" + outfile.getAbsolutePath(),
        };

        Assert.assertEquals(runPicardCommandLine(args), 0);

        final MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Comparable<?>> output = new MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Comparable<?>>();
        output.read(new FileReader(outfile));

        for (final CollectQualityYieldMetrics.QualityYieldMetrics metrics : output.getMetrics()) {
                Assert.assertEquals(metrics.TOTAL_READS, 52);
                Assert.assertEquals(metrics.PF_READS, 52);
                Assert.assertEquals(metrics.READ_LENGTH, 101);
                Assert.assertEquals(metrics.TOTAL_BASES, 5252);
                Assert.assertEquals(metrics.PF_BASES, 5252);
                Assert.assertEquals(metrics.Q20_BASES, 3532);
                Assert.assertEquals(metrics.PF_Q20_BASES, 3532);
                Assert.assertEquals(metrics.Q30_BASES, 3145);
                Assert.assertEquals(metrics.PF_Q30_BASES, 3145);
                Assert.assertEquals(metrics.Q20_EQUIVALENT_YIELD, 6497);
                Assert.assertEquals(metrics.PF_Q20_EQUIVALENT_YIELD, 6497);
        }
    }
}