diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java index 1eba893fc..14c1cd59d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java @@ -348,7 +348,7 @@ public class LikelihoodCalculationEngine { } } } - + // add all filtered reads to the NO_CALL list because they weren't given any likelihoods for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) { // only count the read if it overlaps the event, otherwise it is not added to the output read list at all diff --git a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java index 24ffde9c3..93099f82a 100755 --- a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java @@ -21,7 +21,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest { for ( final int nct : Arrays.asList(1, 2) ) { // tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct }); //// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct }); - tests.add(new Object[]{ "BOTH", "78ce72d8f9d029313f5f2ceb02bb9822", nt, nct }); + tests.add(new Object[]{ "BOTH", "f8184e336dec7632408aa9afa98e6914", nt, nct }); } return tests.toArray(new Object[][]{});