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More bug fixes on the way to passing all tests

This commit is contained in:
Mark DePristo 2011-11-15 17:38:12 -05:00
parent 0be23aae4e
commit df415da4ab
2 changed files with 1 additions and 55 deletions
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5
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
View File

@ -219,12 +219,9 @@ public class GenotypeCollection implements List<Genotype> {
public Genotype get(final String sampleName) {
buildCache();
Integer offset = sampleNameToOffset.get(sampleName);
if ( offset == null )
throw new IllegalArgumentException("Sample " + sampleName + " not found in this GenotypeCollection");
return genotypes.get(offset);
return offset == null ? null : genotypes.get(offset);
}
@Override
public int indexOf(final Object o) {
return genotypes.indexOf(o);

51
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
View File

@ -1,51 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
public class MergeMNPsIntegrationTest extends WalkerTest {
public static String baseTestString(String reference, String VCF, int maxDistMNP) {
return "-T MergeMNPs" +
" -R " + reference +
" --variant:vcf " + validationDataLocation + VCF +
" --maxGenomicDistanceForMNP " + maxDistMNP +
" -o %s" +
" -NO_HEADER";
}
@Test
public void test1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
+ " -L chr20:556259-756570",
1,
Arrays.asList("7f11f7f75d1526077f0173c7ed1fc6c4"));
executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
}
@Test
public void test2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
+ " -L chr20:556259-756570",
1,
Arrays.asList("53dd312468296826bdd3c22387390c88"));
executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
}
@Test
public void test3() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
+ " -L chr20:556259-756570",
1,
Arrays.asList("e26f92d2fb9f4eaeac7f9d8ee27410ee"));
executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
}
}