diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index e6dc319d1..c2380558a 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -362,13 +362,11 @@ public class VariantContextAdaptors { case Silent: attrs.put("VC","Silent"); break; case Missense: attrs.put("VC","Missense"); break; case Nonsense: attrs.put("VC","Nonsense"); break; - case Splice: attrs.put("VC","Splice_site"); break; + case Splice_site: attrs.put("VC","Splice_site"); break; case miRNA: attrs.put("VC","miRNA"); break; case Frameshift: attrs.put("VC","Frameshift"); break; case Inframe: attrs.put("VC","Inframe"); break; case Stop_deletion: attrs.put("VC","Stop_codon_deletion"); - case Splice_site_deletion: attrs.put("VC","Splice_site_deletion"); - case Splice_site_insertion: attrs.put("VC","Splice_site_insertion"); case Unclassified: attrs.put("VC","Unclassified"); default: } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java index 8fd9889b6..7b561f8c5 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java @@ -56,8 +56,8 @@ public class MafFeature implements Feature { }; public enum Classification { - Unclassified, Intergenic,Intron,Noncoding_transcript,UTR3,UTR5,Flank5,Silent,Missense, Nonsense, Splice, miRNA, - Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start,Splice_site_deletion,Splice_site_insertion + Unclassified, Intergenic,Intron,Noncoding_transcript,UTR3,UTR5,Flank5,Silent,Missense, Nonsense, Splice_site, miRNA, + Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start } private Type type = Type.UNKNOWN; @@ -221,15 +221,16 @@ public class MafFeature implements Feature { if ( s.equals("Non-coding_Transcript")) { classification = Classification.Noncoding_transcript; return; } if ( s.equals("Missense") || s.equals("Missense_Mutation") ) { classification = Classification.Missense ; return; } if ( s.equals("Nonsense_Mutation") ) { classification = Classification.Nonsense ; return; } - if ( s.equals("Splice_Site") ) { classification = Classification.Splice ; return; } + if ( s.equals("Splice_Site") ) { classification = Classification.Splice_site ; return; } if ( s.equals("miRNA") ) { classification = Classification.miRNA ; return; } if ( s.equals("Frame_Shift_Ins") ) { classification = Classification.Frameshift ; return; } if ( s.equals("Frame_Shift_Del") ) { classification = Classification.Frameshift ; return; } if ( s.equals("In_Frame_Ins") ) { classification = Classification.Inframe ; return; } if ( s.equals("In_Frame_Del") ) { classification = Classification.Inframe ; return; } if ( s.equals("Stop_Codon_Del") ) { classification = Classification.Stop_deletion ; return; } - if ( s.equals("Splice_Site_Del") ) { classification = Classification.Splice_site_deletion ; return; } - if ( s.equals("Splice_Site_Ins") ) { classification = Classification.Splice_site_insertion ; return; } + if ( s.equals("Splice_Site_Del") ) { classification = Classification.Splice_site ; return; } + if ( s.equals("Splice_Site_Ins") ) { classification = Classification.Splice_site ; return; } + if ( s.equals("Splice_Site_SNP") ) { classification = Classification.Splice_site ; return; } if ( s.equals("Promoter") ) { classification = Classification.Promoter ; return; } if ( s.equals("De_novo_Start") ) { classification = Classification.De_novo_start ; return; } if ( s.equals("TX-REF-MISMATCH") ) { classification = Classification.Unclassified ; return; }