From 6e6ad365238d503b8acd71ae0ceb860fa8c02a71 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 8 Jul 2010 06:26:52 +0000 Subject: [PATCH] reallow MNP events through git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/features/vcf4/VCF4Codec.java | 13 ++++++------- .../sequenom/PickSequenomProbesIntegrationTest.java | 4 ++-- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java index 1d30b64df..1d12f39d1 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java @@ -387,7 +387,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec { // find out our current location, and clip the alleles down to their minimum length Pair> locAndAlleles; - if ( hasIndel(alleles) ) { + if ( !isSingleNucleotideEvent(alleles) ) { attributes.put(ORIGINAL_ALLELE_LIST,alleles); locAndAlleles = clipAlleles(contig, pos, ref, alleles); } else { @@ -405,13 +405,12 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec { return new VariantContext(name, locAndAlleles.first, locAndAlleles.second, genotypes, qual, filters, attributes); } - private boolean hasIndel(List alleles) { - int lengthOfFirstEntry = alleles.get(0).length(); - for ( int i = 1; i < alleles.size(); i++ ) { - if ( alleles.get(i).length() != lengthOfFirstEntry ) - return true; + private boolean isSingleNucleotideEvent(List alleles) { + for ( Allele a : alleles ) { + if ( a.length() > 1 ) + return false; } - return false; + return true; } class VCFParserException extends StingException { diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java index 91329e894..348f27880 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java @@ -11,7 +11,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { String testVCF = validationDataLocation + "complexExample.vcf"; String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("368f6f61e7a99b33f74aab2cf055554e")); + Arrays.asList("0f356354a4a78ff62b2848431ec11262")); executeTest("Test probes", spec); } @@ -26,4 +26,4 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { Arrays.asList("cb1f57e8bcaec4b599be075b6d5288a1")); executeTest("Test probes", spec); } -} \ No newline at end of file +}