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Minor updates to test code

This commit is contained in:
Mark DePristo 2012-06-06 14:07:07 -04:00
parent 54817f8d16
commit cfd1e50068
2 changed files with 4 additions and 3 deletions
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2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
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@ -291,8 +291,6 @@ public class VariantContextTestProvider {
private static void addGenotypes( final VariantContext site) { private static void addGenotypes( final VariantContext site) {
final GenotypesContext gc = new GenotypesContext();
// test ref/ref // test ref/ref
final Allele ref = site.getReference(); final Allele ref = site.getReference();
final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null; final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null;

5
public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java
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@ -55,7 +55,10 @@ public class VariantContextWritersUnitTest extends BaseTest {
@BeforeSuite @BeforeSuite
public void before() throws IOException { 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(); dictionary = seq.getSequenceDictionary();
VariantContextTestProvider.initializeTests(); VariantContextTestProvider.initializeTests();
} }