/*
* The MIT License
*
* Copyright (c) 2013 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.metrics;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.metrics.MetricsFile;
import org.testng.Assert;
import org.testng.annotations.AfterTest;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import picard.analysis.CollectRrbsMetrics;
import picard.analysis.RrbsSummaryMetrics;
import java.io.File;
import java.io.FileReader;
import java.lang.Exception;import java.lang.Integer;import java.lang.String;import java.util.ArrayList;
import java.util.List;
/**
* @author jgentry@broadinstitute.org
*/
public class CollectRrbsMetricsTest {
public static final String CHR_M_SAM = "testdata/picard/metrics/chrMReads.sam";
public static final String CHR_M_REFERENCE ="testdata/picard/metrics/chrM.reference.fasta";
private File rootTestDir;
@BeforeTest
private void setUp() throws Exception {
rootTestDir = File.createTempFile("crmt.", ".tmp");
Assert.assertTrue(rootTestDir.delete());
Assert.assertTrue(rootTestDir.mkdir());
}
@AfterTest
private void tearDown() {
IOUtil.deleteDirectoryTree(rootTestDir);
}
@Test
public void chrMReads() throws Exception {
final MetricsFile<RrbsSummaryMetrics, ?> metricsFile = getSummaryFile(CHR_M_SAM, CHR_M_REFERENCE, rootTestDir + "/READ_TEST", new ArrayList<String>());
final RrbsSummaryMetrics metrics = metricsFile.getMetrics().get(0);
Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
Assert.assertEquals(metrics.CPG_BASES_CONVERTED.intValue(), 1);
Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED, 0.2);
Assert.assertEquals(metrics.MEAN_CPG_COVERAGE, 1.666667);
Assert.assertEquals(metrics.MEDIAN_CPG_COVERAGE.intValue(), 2);
Assert.assertEquals(metrics.READS_WITH_NO_CPG.intValue(), 1);
Assert.assertEquals(metrics.READS_IGNORED_SHORT.intValue(), 1);
Assert.assertEquals(metrics.READS_IGNORED_MISMATCHES.intValue(), 1);
}
private MetricsFile<RrbsSummaryMetrics, ?> getSummaryFile(final String input, final String reference, final String prefix,
final List<String> sequences) throws Exception {
final List<String> argList = new ArrayList<String>();
argList.add("INPUT=" + input);
argList.add("METRICS_FILE_PREFIX=" + prefix);
argList.add("REFERENCE=" + reference);
for (final String sequence : sequences) {
argList.add("SEQUENCE_NAMES=" + sequence);
}
final String[] args = new String[argList.size()];
argList.toArray(args);
Assert.assertEquals(new CollectRrbsMetrics().instanceMain(args), 0);
final MetricsFile<RrbsSummaryMetrics, ?> retVal = new MetricsFile<RrbsSummaryMetrics, Integer>();
retVal.read(new FileReader(prefix + ".rrbs_summary_metrics"));
return retVal;
}
}