From c4ae9c6cfbd48233e6756654fd5dc837d51efa3c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 19:22:02 -0400 Subject: [PATCH] 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. --- .../ValidateVariantsIntegrationTest.java | 10 ++++++++ .../sting/utils/HaplotypeUnitTest.java | 24 +++++++++---------- .../VariantJEXLContextUnitTest.java | 5 +--- 3 files changed, 23 insertions(+), 16 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java index 3277f5060..6a3d755d7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -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); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java index ec08d97c5..161eefa8f 100644 --- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java @@ -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 diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java index 6f5756bdc..8f03f1d38 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java @@ -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");