From e94e6ba101fc30f3364782db2cec5efc3bffe5f3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 8 Oct 2011 08:47:58 -0700 Subject: [PATCH] A UnitTest to ensure that the order of alleles is maintained -> A, C, T and A, T, C are different and must be maintained. The constructors were doing this appropriately, so nothing needed to be changed --- .../variantcontext/VariantContextUnitTest.java | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java index 663eb9ef6..cee7a4782 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -11,12 +11,13 @@ import org.testng.annotations.BeforeSuite; import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; +import java.util.ArrayList; import java.util.Arrays; import java.util.List; public class VariantContextUnitTest extends BaseTest { - Allele A, Aref, T, Tref; + Allele A, Aref, C, T, Tref; Allele del, delRef, ATC, ATCref; // A [ref] / T at 10 @@ -45,6 +46,7 @@ public class VariantContextUnitTest extends BaseTest { delRef = Allele.create("-", true); A = Allele.create("A"); + C = Allele.create("C"); Aref = Allele.create("A", true); T = Allele.create("T"); Tref = Allele.create("T", true); @@ -132,6 +134,16 @@ public class VariantContextUnitTest extends BaseTest { Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC); } + @Test + public void testMultipleSNPAlleleOrdering() { + final List allelesNaturalOrder = Arrays.asList(Aref, C, T); + final List allelesUnnaturalOrder = Arrays.asList(Aref, T, C); + VariantContext naturalVC = new VariantContext("natural", snpLoc, snpLocStart, snpLocStop, allelesNaturalOrder); + VariantContext unnaturalVC = new VariantContext("unnatural", snpLoc, snpLocStart, snpLocStop, allelesUnnaturalOrder); + Assert.assertEquals(new ArrayList(naturalVC.getAlleles()), allelesNaturalOrder); + Assert.assertEquals(new ArrayList(unnaturalVC.getAlleles()), allelesUnnaturalOrder); + } + @Test public void testCreatingSNPVariantContext() {