From 84ebceb9a63930f39c6c8ca98ba3670c71f1e21a Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 22 Apr 2010 02:05:10 +0000 Subject: [PATCH] Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/VariantContextAdaptors.java | 2 ++ .../sting/oneoffprojects/walkers/IndelDBRateWalker.java | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index f9ea154ad..8fb9f9ba3 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -133,6 +133,7 @@ public class VariantContextAdaptors { // -------------------------------------------------------------------------------------------------------------- private static class RodVCFAdaptor extends VCAdaptor { + // WARNING: do not use this method if you have anything other than point mutations in your VCF VariantContext convert(String name, Object input) { return vcfToVariantContext(name, ((RodVCF)input).getRecord(), null); } @@ -143,6 +144,7 @@ public class VariantContextAdaptors { } private static class VCFRecordAdaptor extends VCAdaptor { + // WARNING: do not use this method if you have anything other than point mutations in your VCF VariantContext convert(String name, Object input) { return vcfToVariantContext(name, (VCFRecord)input, null); } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java index 68a99f026..df2aebbbc 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java @@ -86,7 +86,7 @@ public class IndelDBRateWalker extends RodWalker tracker.getReferenceMetaData("eval").size() != 0 ? tracker.getReferenceMetaData("eval").get(0) : null ; VariantContext evalContext; if ( eval != null ) { - evalContext = VariantContextAdaptors.toVariantContext("eval",eval); + evalContext = VariantContextAdaptors.toVariantContext("eval",eval,ref); } else { evalContext = null; }