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Forgot to update VCF4 unit test. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3853 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-07-22 16:25:51 +00:00
parent 485023ba8e
commit 98caedb5f0
1 changed files with 5 additions and 23 deletions
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28
java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java
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@ -201,26 +201,8 @@ public class VCF4UnitTest extends BaseTest {
testSetup.codec.decode(twoFewInfoLine);
}
// test that the variant context adds attributes for the original alleles when clipped
String clippedAlleleLine = "20\t14370\trs6054257\tGGG\tG\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|1:48:1:51,51\t0|0:48:1:51,51\t0|0:48:1:51,51";
@Test
public void testClippedAllelesAddedAsAnnotation() {
// TODO - either modify or kill this test
/* TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
VariantContext context = (VariantContext)testSetup.codec.decode(clippedAlleleLine);
Assert.assertTrue(context.hasAttribute(VCF4Codec.ORIGINAL_ALLELE_LIST));
List<Allele> alleles = (List<Allele>)context.getAttribute(VCF4Codec.ORIGINAL_ALLELE_LIST);
Assert.assertEquals("Expected allele list of 2, got " + alleles.size(),2,alleles.size());
Assert.assertTrue(alleles.get(0).basesMatch("GGG"));
Assert.assertTrue(alleles.get(1).basesMatch("G"));
*/ }
// test that when we don't clip the alleles, we don't see the annotation
@Test
public void testNoClippedAllelesNoAddedAsAnnotation() {
TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
VariantContext context = (VariantContext)testSetup.codec.decode(twoFewInfoLine);
}
// test that we're getting the right genotype for a multi-base polymorphism
String MNPLine = "20\t14370\trs6054257\tGG\tAT\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.";
@Test
@ -340,7 +322,7 @@ public class VCF4UnitTest extends BaseTest {
alleles.add(Allele.create("GT",false));
Pair<GenomeLoc, List<Allele>> locAndList = VCF4Codec.clipAlleles("1",1,ref,alleles);
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",2,3)));
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",1,3)));
// we know the ordering
//System.err.println(locAndList.second.get(0).toString());
@ -364,7 +346,7 @@ public class VCF4UnitTest extends BaseTest {
alleles.add(Allele.create("GGGT",false));
Pair<GenomeLoc, List<Allele>> locAndList = VCF4Codec.clipAlleles("1",1,ref,alleles);
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",2,5)));
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",1,5)));
// we know the ordering
//System.err.println(locAndList.second.get(0).toString());
@ -388,7 +370,7 @@ public class VCF4UnitTest extends BaseTest {
alleles.add(Allele.create("GG",false));
Pair<GenomeLoc, List<Allele>> locAndList = VCF4Codec.clipAlleles("1",1,ref,alleles);
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",2,4)));
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",1,4)));
// we know the ordering
Assert.assertTrue(locAndList.second.get(0).toString().equals("GGG*"));
@ -410,7 +392,7 @@ public class VCF4UnitTest extends BaseTest {
alleles.add(Allele.create("GGG",false));
Pair<GenomeLoc, List<Allele>> locAndList = VCF4Codec.clipAlleles("1",1,ref,alleles);
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",2,4)));
Assert.assertTrue(locAndList.first.equals(GenomeLocParser.createGenomeLoc("1",1,4)));
// we know the ordering
Assert.assertTrue(locAndList.second.get(0).toString().equals("GGG*"));