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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
This commit is contained in:
ebanks 2010-04-22 02:05:10 +00:00
parent e7334ec11f
commit 84ebceb9a6
2 changed files with 3 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -133,6 +133,7 @@ public class VariantContextAdaptors {
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
private static class RodVCFAdaptor extends VCAdaptor { 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) { VariantContext convert(String name, Object input) {
return vcfToVariantContext(name, ((RodVCF)input).getRecord(), null); return vcfToVariantContext(name, ((RodVCF)input).getRecord(), null);
} }
@ -143,6 +144,7 @@ public class VariantContextAdaptors {
} }
private static class VCFRecordAdaptor extends VCAdaptor { 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) { VariantContext convert(String name, Object input) {
return vcfToVariantContext(name, (VCFRecord)input, null); return vcfToVariantContext(name, (VCFRecord)input, null);
} }

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
View File

@ -86,7 +86,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
tracker.getReferenceMetaData("eval").size() != 0 ? tracker.getReferenceMetaData("eval").get(0) : null ; tracker.getReferenceMetaData("eval").size() != 0 ? tracker.getReferenceMetaData("eval").get(0) : null ;
VariantContext evalContext; VariantContext evalContext;
if ( eval != null ) { if ( eval != null ) {
evalContext = VariantContextAdaptors.toVariantContext("eval",eval); evalContext = VariantContextAdaptors.toVariantContext("eval",eval,ref);
} else { } else {
evalContext = null; evalContext = null;
} }