From cfd1e500680598fa7d46f125a99624dfede3de9e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 6 Jun 2012 14:07:07 -0400 Subject: [PATCH] Minor updates to test code --- .../utils/variantcontext/VariantContextTestProvider.java | 2 -- .../variantcontext/writer/VariantContextWritersUnitTest.java | 5 ++++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index 22ec66cd9..9b05bd30b 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -291,8 +291,6 @@ public class VariantContextTestProvider { private static void addGenotypes( final VariantContext site) { - final GenotypesContext gc = new GenotypesContext(); - // test ref/ref final Allele ref = site.getReference(); final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java index ce52d4869..9ecffe939 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java @@ -55,7 +55,10 @@ public class VariantContextWritersUnitTest extends BaseTest { @BeforeSuite public void before() throws IOException { - IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + final File source = new File(b37KGReference); + //final File source = new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"); + IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(source); + //IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); dictionary = seq.getSequenceDictionary(); VariantContextTestProvider.initializeTests(); }