From a5aaa14aaa2465d91cc82d308ae32311073bca80 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 7 Oct 2012 01:19:52 -0400 Subject: [PATCH] Fix for GSA-601: Indels dropped during liftover. This was a true bug that was an effect of the switch over to the non-null representation of alleles in the VariantContext. Unfortunately, this tool didn't have integration tests - but it does now. --- .../gatk/walkers/variantutils/FilterLiftedVariants.java | 2 +- .../variantutils/LiftoverVariantsIntegrationTest.java | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index f89bcb2a7..92d6e686b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -75,7 +75,7 @@ public class FilterLiftedVariants extends RodWalker { boolean failed = false; byte[] recordRef = vc.getReference().getBases(); for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) { - if ( recordRef[i] != ref[i + (vc.isPointEvent() ? 0 : 1)] ) { + if ( recordRef[i] != ref[i] ) { failed = true; break; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index e14580ead..bc69ba8f7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -61,4 +61,13 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { Arrays.asList("7e7bad0e1890753a01303c09a38ceb8d")); executeTest("test hg18 to hg19, unsorted", spec); } + + @Test + public void testLiftoverFilteringOfIndels() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T FilterLiftedVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "liftover_indel_test.vcf", + 1, + Arrays.asList("b9280bb4f310c72284251bc6f2bf2bb2")); + executeTest("test liftover filtering of indels", spec); + } }