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With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.

This commit is contained in:
Eric Banks 2012-07-29 19:22:02 -04:00
parent 99b15b2b3a
commit c4ae9c6cfb
3 changed files with 23 additions and 16 deletions
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10
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
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@ -125,4 +125,14 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
executeTest("test bad ref allele in deletion", spec);
}
@Test
public void testComplexEvents() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("complexEvents.vcf", "ALL"),
0,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")
);
executeTest("test validating complex events", spec);
}
}

24
public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
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@ -53,11 +53,11 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases);
h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA";
basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases);
h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases);
}
@Test
@ -68,11 +68,11 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases);
h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA";
basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases);
h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases);
}
@Test
@ -102,11 +102,11 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases);
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases);
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC";
basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases);
}
@Test
@ -121,11 +121,11 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases);
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases);
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC";
basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases);
}
@Test

5
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
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@ -56,7 +56,7 @@ public class VariantJEXLContextUnitTest extends BaseTest {
Allele A, Aref, T, Tref;
Allele del, delRef, ATC, ATCref;
Allele ATC, ATCref;
// A [ref] / T at 10
GenomeLoc snpLoc;
@ -84,9 +84,6 @@ public class VariantJEXLContextUnitTest extends BaseTest {
@BeforeMethod
public void before() {
del = Allele.create("-");
delRef = Allele.create("-", true);
A = Allele.create("A");
Aref = Allele.create("A", true);
T = Allele.create("T");