diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 8ae2eed82..1ab3b10c4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -135,14 +135,6 @@ public class RecalDatum { 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() { return estimatedQReported; } diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java index 715acad03..0f0c74362 100644 --- a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java @@ -106,6 +106,11 @@ public class RecalDatumUnitTest extends BaseTest { Assert.assertEquals(datum.getEstimatedQReportedAsByte(), cfg.getReportedQual()); BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalQuality(), cfg.getErrorRatePhredScaled()); 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") @@ -145,10 +150,32 @@ public class RecalDatumUnitTest extends BaseTest { cfg.exTotal++; 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.increment(10, 5); cfg.exError += 5; cfg.exTotal += 10; assertBasicFeaturesOfRecalDatum(datum, cfg); } + + @Test + public void testNoObs() { + final RecalDatum rd = new RecalDatum(0, 0, (byte)10); + Assert.assertEquals(rd.getEmpiricalErrorRate(), 0.0); + } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java index d597b9f2c..b190f2ff2 100644 --- a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java @@ -21,6 +21,14 @@ import java.util.*; * @since 4/21/12 */ 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) public void testOutput() { final int length = 100; @@ -86,12 +94,12 @@ public class RecalibrationReportUnitTest { final int[] covariates = rc.getKeySet(offset, errorMode); final int randomMax = errorMode == EventType.BASE_SUBSTITUTION ? 10000 : 100000; - rgTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.index); - qualTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.index); + rgTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.index); + qualTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.index); nKeys += 2; for (int j = 0; j < optionalCovariates.size(); j++) { final NestedIntegerArray 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++; } }