package picard.analysis;
import htsjdk.samtools.metrics.MetricsFile;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashSet;
public class CollectOxoGMetricsTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam/");
private static final File SAM_FILE = new File(TEST_DATA_DIR, "summary_alignment_stats_test.sam");
private static final File REFERENCE_SEQUENCE = new File(TEST_DATA_DIR, "merger.fasta");
@Test
public void testCollectOxoGMetrics() throws IOException {
final File outputFile = File.createTempFile("test", ".oxo_g_metrics", TEST_DATA_DIR);
outputFile.deleteOnExit();
final String[] args = new String[]{
"INPUT=" + SAM_FILE.getAbsolutePath(),
"OUTPUT=" + outputFile.getAbsolutePath(),
"REFERENCE_SEQUENCE=" + REFERENCE_SEQUENCE.getAbsolutePath()
};
CollectOxoGMetrics collectOxoGMetrics = new CollectOxoGMetrics();
Assert.assertEquals(collectOxoGMetrics.instanceMain(args), 0,
"Can't process " + SAM_FILE.getAbsolutePath() + " correctly");
final MetricsFile<CollectOxoGMetrics.CpcgMetrics, Comparable<?>> output = new MetricsFile<>();
output.read(new FileReader(outputFile));
final int metricsNumber = 4; // metrics number for testing (randomly chosen) that corresponds "TCT" context string.
final CollectOxoGMetrics.CpcgMetrics metrics = output.getMetrics().get(metricsNumber);
Assert.assertEquals(metrics.SAMPLE_ALIAS, "Hi,Momma!");
Assert.assertEquals(metrics.LIBRARY, "whatever");
Assert.assertEquals(metrics.CONTEXT, "TCT");
Assert.assertEquals(metrics.TOTAL_SITES, 3);
Assert.assertEquals(metrics.TOTAL_BASES, 3);
Assert.assertEquals(metrics.REF_NONOXO_BASES, 0);
Assert.assertEquals(metrics.REF_OXO_BASES, 3);
Assert.assertEquals(metrics.REF_TOTAL_BASES, 3);
Assert.assertEquals(metrics.ALT_NONOXO_BASES, 0);
Assert.assertEquals(metrics.ALT_OXO_BASES, 0);
Assert.assertEquals(metrics.OXIDATION_ERROR_RATE, 0.333333);
Assert.assertEquals(metrics.OXIDATION_Q, 4.771213);
Assert.assertEquals(metrics.C_REF_REF_BASES, 0);
Assert.assertEquals(metrics.G_REF_REF_BASES, 3);
Assert.assertEquals(metrics.C_REF_ALT_BASES, 0);
Assert.assertEquals(metrics.G_REF_ALT_BASES, 0);
Assert.assertEquals(metrics.C_REF_OXO_ERROR_RATE, Double.NaN);
Assert.assertEquals(metrics.C_REF_OXO_Q, Double.NaN);
Assert.assertEquals(metrics.G_REF_OXO_ERROR_RATE, Double.NaN);
Assert.assertEquals(metrics.G_REF_OXO_Q, Double.NaN);
}
@DataProvider(name = "RightOptions")
public static Object[][] rightOptions() {
final HashSet<String> rightContext1 = new HashSet<>();
rightContext1.add("ACC");
final HashSet<String> rightContext2 = new HashSet<>();
rightContext2.add("AACAA");
rightContext2.add("ATCAT");
return new Object[][] {
{5, 10, 1, rightContext1}, //contextSize = 1
{10, 10, 2, rightContext2} //contextSize = 2
};
}
@Test(dataProvider = "RightOptions")
public void testPositiveCustomCommandLineValidation(final int minimumInsertSize,
final int maximumInsertSize,
final int contextSize,
final HashSet<String> context) throws Exception {
final CollectOxoGMetrics collectOxoGMetrics = getCollectOxoGMetrics(minimumInsertSize, maximumInsertSize, contextSize, context);
Assert.assertNull(collectOxoGMetrics.customCommandLineValidation());
Assert.assertEquals(collectOxoGMetrics.MINIMUM_INSERT_SIZE, minimumInsertSize);
Assert.assertEquals(collectOxoGMetrics.MAXIMUM_INSERT_SIZE, maximumInsertSize);
Assert.assertEquals(collectOxoGMetrics.CONTEXT_SIZE, contextSize);
Assert.assertEquals(collectOxoGMetrics.CONTEXTS, context);
}
@DataProvider(name = "WrongOptions")
public static Object[][] wrongOptions() {
//Middle base of context sequence must be C
final HashSet<String> wrongContext1 = new HashSet<>();
wrongContext1.add("AAC");
//Middle base of context sequence must be C
final HashSet<String> wrongContext2 = new HashSet<>();
wrongContext2.add("AAGAA");
wrongContext2.add("ATCAT");
final HashSet<String> rightContext1 = new HashSet<>();
rightContext1.add("ACC");
return new Object[][] {
{5, 10, 1, wrongContext1, "Middle base of context sequence AAC must be C"},
{10, 10, 1, wrongContext2, "Context AAGAA is not 3 long as implied by CONTEXT_SIZE=1"},
{10, 5, 1, rightContext1, "MAXIMUM_INSERT_SIZE cannot be less than MINIMUM_INSERT_SIZE"}, //min insert size > max insert size
{-5, 10, 1, rightContext1, "MINIMUM_INSERT_SIZE cannot be negative"} //negative insert size
};
}
@Test(dataProvider = "WrongOptions")
public void testNegativeCustomCommandLineValidation(final int minimumInsertSize,
final int maximumInsertSize,
final int contextSize,
final HashSet<String> context,
final String expectedMessage) throws Exception {
final CollectOxoGMetrics collectOxoGMetrics = getCollectOxoGMetrics(minimumInsertSize, maximumInsertSize, contextSize, context);
Assert.assertNotNull(collectOxoGMetrics.customCommandLineValidation());
Assert.assertEquals(collectOxoGMetrics.customCommandLineValidation()[0], expectedMessage);
}
private static CollectOxoGMetrics getCollectOxoGMetrics(final int minimumInsertSize,
final int maximumInsertSize,
final int contextSize,
final HashSet<String> context) {
final CollectOxoGMetrics collectOxoGMetrics = new CollectOxoGMetrics();
collectOxoGMetrics.MINIMUM_INSERT_SIZE = minimumInsertSize;
collectOxoGMetrics.MAXIMUM_INSERT_SIZE = maximumInsertSize;
collectOxoGMetrics.CONTEXT_SIZE = contextSize;
collectOxoGMetrics.CONTEXTS = context;
return collectOxoGMetrics;
}
}