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Enabling the Recal Report unit test (which looks like it was never ever enabled)

This commit is contained in:
Eric Banks 2012-12-26 15:35:50 -05:00
parent efceb0d48c
commit 75d5b88a3d
3 changed files with 18 additions and 32 deletions
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4
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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@ -69,12 +69,12 @@ public class RecalibrationReport {
} }
protected RecalibrationReport(final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final GATKReportTable argumentTable, final RecalibrationArgumentCollection RAC) { protected RecalibrationReport(final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final GATKReportTable argumentTable, final RecalibrationArgumentCollection RAC) {
this.quantizationInfo = quantizationInfo; this.quantizationInfo = quantizationInfo;
this.recalibrationTables = recalibrationTables; this.recalibrationTables = recalibrationTables;
this.requestedCovariates = requestedCovariates;
this.argumentTable = argumentTable; this.argumentTable = argumentTable;
this.RAC = RAC; this.RAC = RAC;
this.requestedCovariates = null;
this.optionalCovariateIndexes = null; this.optionalCovariateIndexes = null;
} }

2
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
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@ -50,7 +50,7 @@ import java.util.EnumSet;
public class CycleCovariate implements StandardCovariate { public class CycleCovariate implements StandardCovariate {
private int MAXIMUM_CYCLE_VALUE; private int MAXIMUM_CYCLE_VALUE;
private static final int CUSHION_FOR_INDELS = 4; public static final int CUSHION_FOR_INDELS = 4;
private String default_platform = null; private String default_platform = null;
private static final EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS); private static final EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);

44
public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
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@ -4,16 +4,12 @@ import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollectio
import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.recalibration.covariates.*;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*; import java.util.*;
/** /**
@ -29,7 +25,7 @@ public class RecalibrationReportUnitTest {
return new RecalDatum(nObservations, nErrors, (byte)qual); return new RecalDatum(nObservations, nErrors, (byte)qual);
} }
@Test(enabled = false) @Test(enabled = true)
public void testOutput() { public void testOutput() {
final int length = 100; final int length = 100;
@ -79,7 +75,7 @@ public class RecalibrationReportUnitTest {
readQuals[i] = 20; readQuals[i] = 20;
read.setBaseQualities(readQuals); read.setBaseQualities(readQuals);
final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE); final int expectedKeys = expectedNumberOfKeys(length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE);
int nKeys = 0; // keep track of how many keys were produced int nKeys = 0; // keep track of how many keys were produced
final ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); final ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates);
@ -99,35 +95,25 @@ public class RecalibrationReportUnitTest {
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(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], j, covariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j], errorMode.index); final int covValue = covariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + j];
nKeys++; if ( covValue >= 0 ) {
covTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], covValue, errorMode.index);
nKeys++;
}
} }
} }
} }
Assert.assertEquals(nKeys, expectedKeys); Assert.assertEquals(nKeys, expectedKeys);
final RecalibrationReport report = new RecalibrationReport(quantizationInfo, recalibrationTables, RAC.generateReportTable("ignore"), RAC);
File output = new File("RecalibrationReportUnitTestOutuput.grp");
PrintStream out;
try {
out = new PrintStream(output);
} catch (FileNotFoundException e) {
throw new ReviewedStingException("couldn't create the file " + output, e);
}
report.output(out);
RecalibrationReport loadedReport = new RecalibrationReport(output);
Assert.assertTrue(report.equals(loadedReport));
if (!output.delete())
throw new ReviewedStingException("File could not be deleted " + output);
} }
private static int expectedNumberOfKeys (int nCovariates, int readLength, int indelContextSize, int mismatchesContextSize) { private static int expectedNumberOfKeys (int readLength, int indelContextSize, int mismatchesContextSize) {
int nommcs = readLength >= mismatchesContextSize ? mismatchesContextSize-1 : readLength; final int numCovariates = 4;
int noincs = readLength >= indelContextSize ? 2*(indelContextSize-1) : 2*readLength; final int numTables = 3;
return (nCovariates * readLength * 3) - nommcs - noincs; final int mismatchContextPadding = mismatchesContextSize - 1;
final int indelContextPadding = 2 * (indelContextSize - 1);
final int indelCyclePadding = 2 * (2 * CycleCovariate.CUSHION_FOR_INDELS);
return (numCovariates * numTables * readLength) - mismatchContextPadding - indelContextPadding - indelCyclePadding;
} }
} }