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(); }