From 35543b9cbab7ff489b2eb8fb3bdbf518f9e3cf0d Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 29 Jan 2013 09:47:57 -0500 Subject: [PATCH] updating BQSR integration test values for the PR half of BQSR. --- .../sting/utils/recalibration/BaseRecalibration.java | 4 ---- .../sting/utils/recalibration/RecalDatum.java | 2 +- .../sting/utils/recalibration/RecalibrationReport.java | 2 +- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 8 ++++---- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index ba18f5c96..1f4e92ad7 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -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); - } } } diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 67794c248..0b4441439 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -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); } diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java index bf8f00ca4..e3ab16639 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java @@ -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; } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index b8a409d2f..254bfd92c 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -188,12 +188,12 @@ public class BQSRIntegrationTest extends WalkerTest { public Object[][] createPRTestData() { List tests = new ArrayList(); - 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[][]{});