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Minor cleanup and expansion of the RecalDatum unit tests

This commit is contained in:
Mark DePristo 2012-12-24 13:26:58 -05:00
parent 7ec7a5d6b6
commit 04cc75aaec
3 changed files with 38 additions and 11 deletions
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8
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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@ -135,14 +135,6 @@ public class RecalDatum {
this.estimatedQReported = estimatedQReported; this.estimatedQReported = estimatedQReported;
} }
public static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) {
final Random random = new Random();
final int nObservations = random.nextInt(maxObservations);
final int nErrors = random.nextInt(maxErrors);
final int qual = random.nextInt(QualityUtils.MAX_QUAL_SCORE);
return new RecalDatum(nObservations, nErrors, (byte)qual);
}
public final double getEstimatedQReported() { public final double getEstimatedQReported() {
return estimatedQReported; return estimatedQReported;
} }

27
public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
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@ -106,6 +106,11 @@ public class RecalDatumUnitTest extends BaseTest {
Assert.assertEquals(datum.getEstimatedQReportedAsByte(), cfg.getReportedQual()); Assert.assertEquals(datum.getEstimatedQReportedAsByte(), cfg.getReportedQual());
BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalQuality(), cfg.getErrorRatePhredScaled()); BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalQuality(), cfg.getErrorRatePhredScaled());
BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalErrorRate(), cfg.getErrorRate()); BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalErrorRate(), cfg.getErrorRate());
final double e = datum.getEmpiricalQuality();
Assert.assertTrue(datum.getEmpiricalQualityAsByte() >= Math.floor(e));
Assert.assertTrue(datum.getEmpiricalQualityAsByte() <= Math.ceil(e));
Assert.assertNotNull(datum.toString());
} }
@Test(dataProvider = "RecalDatumTestProvider") @Test(dataProvider = "RecalDatumTestProvider")
@ -145,10 +150,32 @@ public class RecalDatumUnitTest extends BaseTest {
cfg.exTotal++; cfg.exTotal++;
assertBasicFeaturesOfRecalDatum(datum, cfg); assertBasicFeaturesOfRecalDatum(datum, cfg);
datum = cfg.makeRecalDatum();
datum.increment(false);
cfg.exTotal++;
assertBasicFeaturesOfRecalDatum(datum, cfg);
datum = cfg.makeRecalDatum();
datum.incrementNumObservations(2);
cfg.exTotal += 2;
assertBasicFeaturesOfRecalDatum(datum, cfg);
datum = cfg.makeRecalDatum();
datum.incrementNumMismatches(2);
cfg.exError += 2;
assertBasicFeaturesOfRecalDatum(datum, cfg);
datum = cfg.makeRecalDatum(); datum = cfg.makeRecalDatum();
datum.increment(10, 5); datum.increment(10, 5);
cfg.exError += 5; cfg.exError += 5;
cfg.exTotal += 10; cfg.exTotal += 10;
assertBasicFeaturesOfRecalDatum(datum, cfg); assertBasicFeaturesOfRecalDatum(datum, cfg);
} }
@Test
public void testNoObs() {
final RecalDatum rd = new RecalDatum(0, 0, (byte)10);
Assert.assertEquals(rd.getEmpiricalErrorRate(), 0.0);
}
} }

14
public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
View File

@ -21,6 +21,14 @@ import java.util.*;
* @since 4/21/12 * @since 4/21/12
*/ */
public class RecalibrationReportUnitTest { public class RecalibrationReportUnitTest {
private static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) {
final Random random = new Random();
final int nObservations = random.nextInt(maxObservations);
final int nErrors = random.nextInt(maxErrors);
final int qual = random.nextInt(QualityUtils.MAX_QUAL_SCORE);
return new RecalDatum(nObservations, nErrors, (byte)qual);
}
@Test(enabled = false) @Test(enabled = false)
public void testOutput() { public void testOutput() {
final int length = 100; final int length = 100;
@ -86,12 +94,12 @@ public class RecalibrationReportUnitTest {
final int[] covariates = rc.getKeySet(offset, errorMode); final int[] covariates = rc.getKeySet(offset, errorMode);
final int randomMax = errorMode == EventType.BASE_SUBSTITUTION ? 10000 : 100000; final int randomMax = errorMode == EventType.BASE_SUBSTITUTION ? 10000 : 100000;
rgTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.index); rgTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.index);
qualTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.index); qualTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.index);
nKeys += 2; nKeys += 2;
for (int j = 0; j < optionalCovariates.size(); j++) { for (int j = 0; j < optionalCovariates.size(); j++) {
final NestedIntegerArray<RecalDatum> covTable = recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j); final NestedIntegerArray<RecalDatum> covTable = recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j);
covTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], j, covariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j], errorMode.index); covTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], j, covariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j], errorMode.index);
nKeys++; nKeys++;
} }
} }