From bca860723a4ae6d7cfaf242065256951bcb543fe Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 3 Dec 2012 22:01:07 -0500 Subject: [PATCH] Updating tests to handle bad validation data files (that used the wrong qual score encoding); overrides push from stable. --- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 2 ++ .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) 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 de328c825..b15969fba 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 @@ -37,6 +37,7 @@ public class BQSRIntegrationTest extends WalkerTest { " -L " + interval + args + " -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) + + " --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams " -o %s"; } @@ -112,6 +113,7 @@ public class BQSRIntegrationTest extends WalkerTest { " -R " + b36KGReference + " -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" + " -L 1:50,000-80,000" + + " --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams " -o %s", 1, // just one output file UserException.class); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 8ded61af8..959cdd1ce 100755 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -436,8 +436,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testNsInCigar() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1, - Arrays.asList("d6d40bacd540a41f305420dfea35e04a")); + "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1, + Arrays.asList("32f18ba50406cd8c8069ba07f2f89558")); executeTest("test calling on reads with Ns in CIGAR", spec); }