From 00c98ff0cf52fcaf484fc8fd0556085f3fe28605 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 5 Feb 2013 10:41:46 -0500 Subject: [PATCH] Need to reset the static counter before tests are run or else we won't be deterministic. Also need to give credit where credit is due: David was right that this was not a non-deterministic Bamboo failure... --- .../sting/utils/sam/MisencodedBaseQualityReadTransformer.java | 2 +- .../sting/utils/sam/MisencodedBaseQualityUnitTest.java | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java index d22c0bd7b..20e3736f2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java @@ -44,7 +44,7 @@ public class MisencodedBaseQualityReadTransformer extends ReadTransformer { private boolean disabled; private boolean fixQuals; - private static int currentReadCounter = 0; + protected static int currentReadCounter = 0; @Override public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) { diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java index 3b2696554..7a23f0f10 100644 --- a/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java @@ -49,6 +49,8 @@ public class MisencodedBaseQualityUnitTest extends BaseTest { @BeforeMethod public void before() { + // reset the read counter so that we are deterministic + MisencodedBaseQualityReadTransformer.currentReadCounter = 0; header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); }