/*
* 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.illumina;
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.DataProvider;
import org.testng.annotations.Test;
import picard.PicardException;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.List;
import static picard.illumina.CollectIlluminaSummaryMetrics.*;
/**
* @author farjoun@broadinstitute.org
*/
public class CollectIlluminaSummaryMetricsTest {
public static final String TEST_DATA_DIR = "testdata/picard/quality/";
public static final String CHR_M_REFERENCE = TEST_DATA_DIR+"chrM.reference.fasta";
private File rootTestDir;
@BeforeTest
private void setUp() throws Exception {
rootTestDir = File.createTempFile("CollectIlluminaSummaryMetricsTest.", ".tmp");
Assert.assertTrue(rootTestDir.delete());
Assert.assertTrue(rootTestDir.mkdir());
}
@AfterTest
private void tearDown() {
IOUtil.deleteDirectoryTree(rootTestDir);
}
@Test(expectedExceptions = PicardException.class)
public void testIlluminaSummaryReadLengthFail() throws Exception {
getSummaryFile("null",TEST_DATA_DIR+"chrMReadsDiffereingLengths.sam", CHR_M_REFERENCE,"/dev/null");
}
@DataProvider(name="IlluminaSummaryData")
public Object[][] testIlluminaSummaryData() {
return new Object[][]{
{"",TEST_DATA_DIR+"chrMReads.sam", 5, 2, 2, 5*36L, 2*36L, 0L, 0D, (5*36L)/5, 16299L}, // only dups and failing reads
{"",TEST_DATA_DIR+"chrMReadsMated.sam", 2, 2, 0, 2*36L, 2*36L,66L, 66.0D/16299, 36L, 16299L}, // nice paired reads
{"",TEST_DATA_DIR+"chrMReadsMatedRev.sam", 2, 2, 0, 2*36L, 2*36L,66L, 66.0D/16299, 36L, 16299L}, // nice paired reads (reversed order)
{"",TEST_DATA_DIR+"chrMReadsMatedSameStrand.sam", 2, 2, 0, 2*36L, 2*36L,46L, 46.0D/16299, 36L, 16299L}, // nice paired reads (same strand)
{"",TEST_DATA_DIR+"chrMReadsMateUnmapped.sam", 2, 2, 0, 2*36L, 2*36L,2*36L, 2*36.0D/16299, 36L, 16299L}, // one mate is unmapped
{"",TEST_DATA_DIR+"chrMReadsUnMated.sam", 1, 1, 0, 1*36L, 1*36L,1*36L, 1*36.0D/16299, 36L, 16299L}, // one mate is unmapped
{"",TEST_DATA_DIR+"chrMReadsSecondaryAlignSoft.sam", 2, 2, 0, 2*36L, 2*36L,66L, 66.0D/16299, 36L, 16299L}, // secondary read with soft clips
{"",TEST_DATA_DIR+"chrMReadsSupplementalAlignSoft.sam", 2, 2, 0, 2*36L, 2*36L,66L, 66.0D/16299, 36L, 16299L}, // secondary read with soft clips
{TEST_DATA_DIR+"chrM.part.intervallist",
TEST_DATA_DIR+"chrMReadsMated.sam", 2, 2, 0, 2*36L, 2*36L,66L, 66.0D/2000, 36L, 2000L}, // nice paired reads with an interval list
};
}
@Test(dataProvider = "IlluminaSummaryData")
public void testIlluminaSummary(final String intervalFile, final String fileBAM, final Integer TOTAL_READS, final Integer PF_READS, final Integer DUPLICATE_READS,
final Long TOTAL_BASES, final Long PF_BASES, final Long TOTAL_ILMN_BASES, final Double AVERAGE_ILMN_DEPTH, final Long READ_LENGTH, final Long TARGET_REGION) throws Exception {
final IlluminaSummaryMetrics expectedMetric=new IlluminaSummaryMetrics( TOTAL_READS, PF_READS, DUPLICATE_READS, TOTAL_BASES, PF_BASES, TOTAL_ILMN_BASES, AVERAGE_ILMN_DEPTH, READ_LENGTH, TARGET_REGION);
final MetricsFile<IlluminaSummaryMetrics, ?> metricsFile = getSummaryFile(intervalFile,fileBAM, CHR_M_REFERENCE, rootTestDir + "/READ_TEST");
final IlluminaSummaryMetrics metrics = metricsFile.getMetrics().get(0);
Assert.assertEquals(metrics.toString(), expectedMetric.toString());
}
private MetricsFile<IlluminaSummaryMetrics, ?> getSummaryFile(final String intervalFile, final String input, final String reference, final String outputFile) throws Exception {
final List<String> argList = new ArrayList<String>();
argList.add("I=" + input);
argList.add("O=" + outputFile);
argList.add("R=" + reference);
if(!intervalFile.equals("")) argList.add("TARGET_REGION="+intervalFile);
final String[] args = new String[argList.size()];
argList.toArray(args);
Assert.assertEquals(new CollectIlluminaSummaryMetrics().instanceMain(args), 0);
final MetricsFile<IlluminaSummaryMetrics, Integer> retVal = new MetricsFile<IlluminaSummaryMetrics, Integer>();
retVal.read(new FileReader(outputFile));
return retVal;
}
}