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updating BQSR integration test values for the PR half of BQSR.

This commit is contained in:
Ryan Poplin 2013-01-29 09:47:57 -05:00
parent bf25196a0b
commit 35543b9cba
4 changed files with 6 additions and 10 deletions
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4
protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -212,10 +212,6 @@ public class BaseRecalibration {
final byte recalibratedQualityScore = quantizationInfo.getQuantizedQuals().get(recalibratedQual);
quals[offset] = recalibratedQualityScore;
if( quals[offset] > QualityUtils.MAX_REASONABLE_Q_SCORE ) {
System.out.println("A");
//calculateDeltaQCovariates(recalibrationTables, keySet, errorModel, globalDeltaQ, deltaQReported, origQual);
}
}
}

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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@ -225,7 +225,7 @@ public class RecalDatum {
return getEmpiricalQuality(getEstimatedQReported());
}
public final double getEmpiricalQuality(final double conditionalPrior) {
public synchronized final double getEmpiricalQuality(final double conditionalPrior) {
if (empiricalQuality == UNINITIALIZED) {
calcEmpiricalQuality(conditionalPrior);
}

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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@ -255,7 +255,7 @@ public class RecalibrationReport {
final RecalDatum datum = new RecalDatum(nObservations, nErrors, (byte)1);
datum.setEstimatedQReported(estimatedQReported);
//datum.setEmpiricalQuality(empiricalQuality);
//datum.setEmpiricalQuality(empiricalQuality); // don't set the value here because we will want to recompute with a different conditional Q score prior value
return datum;
}

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -188,12 +188,12 @@ public class BQSRIntegrationTest extends WalkerTest {
public Object[][] createPRTestData() {
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{1, new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")});
tests.add(new Object[]{1, new PRTest(" -qq -1", "64622d37e234e57cf472068a00b4ec89")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "735270581d1ee836f3f99d68ecbd5f24")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "1e3b0a11f246a238ac4c06b084142715")});
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")});
tests.add(new Object[]{nct, new PRTest("", "39ecde2c2ba4a7c109e65372618a419a")});
}
return tests.toArray(new Object[][]{});