From 1b0a7757738f13dfffb98cab27826fe2a1a40680 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 2 Jul 2012 15:55:42 -0400 Subject: [PATCH] Disabling bcf2 reading from samtools because it's 1 basis; updating select variants integrationtest --- .../walkers/variantutils/SelectVariantsIntegrationTest.java | 2 +- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 5e674d6c2..59eaa177d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile), 1, - Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b") + Arrays.asList("4386fbb258dcef4437495a37f5a83c53") ); spec.disableShadowBCF(); executeTest("testComplexSelection--" + testfile, spec); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 1eda504db..1e3c799fe 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -59,7 +59,7 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test writing samtools WEx BCF example", spec1); } - @Test + @Test(enabled = false) // TODO disabled because current BCF2 is 1 based public void testReadingSamtoolsWExBCFExample() { String testVCF = privateTestDir + "ex2.bcf"; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";