/*
* The MIT License
*
* Copyright (c) 2010 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;
/**
* Tests multi-level CollectInsertSizeMetrics
*/
public class CollectInsertSizeMetricsTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam/");
public String getCommandLineProgramName() {
return CollectInsertSizeMetrics.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", ".insert_size_metrics");
final File pdf = File.createTempFile("test", ".pdf");
outfile.deleteOnExit();
pdf.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"HISTOGRAM_FILE=" + pdf.getAbsolutePath()
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<InsertSizeMetrics, Comparable<?>> output = new MetricsFile<InsertSizeMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final InsertSizeMetrics metrics : output.getMetrics()) {
Assert.assertEquals(metrics.PAIR_ORIENTATION.name(), "FR");
if (metrics.LIBRARY==null) { // SAMPLE or ALL_READS level
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 41);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 45);
Assert.assertEquals(metrics.READ_PAIRS, 13);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 7);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 7);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 7);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 9);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 11);
}
else if (metrics.LIBRARY.equals("Solexa-41753")) { // one LIBRARY and one READ_GROUP
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 44);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 44);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 44);
Assert.assertEquals(metrics.READ_PAIRS, 2);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 1);
}
else if (metrics.LIBRARY.equals("Solexa-41748") && metrics.READ_GROUP == null) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 40);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 45);
Assert.assertEquals(metrics.READ_PAIRS, 9);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 3);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 3);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 3);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 5);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 5);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 9);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 9);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 11);
}
else if (metrics.LIBRARY.equals("Solexa-41734") && metrics.READ_GROUP == null) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 26);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 41);
Assert.assertEquals(metrics.READ_PAIRS, 9);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 11);
}
else if (metrics.READ_GROUP.equals("62A79AAXX100907.7")) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 41);
Assert.assertEquals(metrics.READ_PAIRS, 4);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 5);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 5);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 11);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 11);
}
else if (metrics.READ_GROUP.equals("62A79AAXX100907.6")) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 41);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 38);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 45);
Assert.assertEquals(metrics.READ_PAIRS, 5);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 3);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 3);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 7);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 7);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 9);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 9);
}
else if (metrics.READ_GROUP.equals("62A79AAXX100907.5")) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 41);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 41);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 41);
Assert.assertEquals(metrics.READ_PAIRS, 1);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 1);
}
else if (metrics.READ_GROUP.equals("62A79AAXX100907.3")) {
Assert.assertEquals((int)metrics.MEDIAN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MIN_INSERT_SIZE, 36);
Assert.assertEquals(metrics.MAX_INSERT_SIZE, 36);
Assert.assertEquals(metrics.READ_PAIRS, 1);
Assert.assertEquals(metrics.WIDTH_OF_10_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_20_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_30_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_40_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_50_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_60_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_70_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_80_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_90_PERCENT, 1);
Assert.assertEquals(metrics.WIDTH_OF_99_PERCENT, 1);
}
else {
Assert.fail("Unexpected metric: " + metrics);
}
}
}
}