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Another change in variant classification values 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5237 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-02-14 17:47:58 +00:00
parent 7f7d7eb2d1
commit 7a11b4f35d
2 changed files with 7 additions and 8 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -362,13 +362,11 @@ public class VariantContextAdaptors {
case Silent: attrs.put("VC","Silent"); break; case Silent: attrs.put("VC","Silent"); break;
case Missense: attrs.put("VC","Missense"); break; case Missense: attrs.put("VC","Missense"); break;
case Nonsense: attrs.put("VC","Nonsense"); 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 miRNA: attrs.put("VC","miRNA"); break;
case Frameshift: attrs.put("VC","Frameshift"); break; case Frameshift: attrs.put("VC","Frameshift"); break;
case Inframe: attrs.put("VC","Inframe"); break; case Inframe: attrs.put("VC","Inframe"); break;
case Stop_deletion: attrs.put("VC","Stop_codon_deletion"); 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"); case Unclassified: attrs.put("VC","Unclassified");
default: default:
} }

11
java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java
View File

@ -56,8 +56,8 @@ public class MafFeature implements Feature {
}; };
public enum Classification { public enum Classification {
Unclassified, Intergenic,Intron,Noncoding_transcript,UTR3,UTR5,Flank5,Silent,Missense, Nonsense, Splice, miRNA, Unclassified, Intergenic,Intron,Noncoding_transcript,UTR3,UTR5,Flank5,Silent,Missense, Nonsense, Splice_site, miRNA,
Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start,Splice_site_deletion,Splice_site_insertion Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start
} }
private Type type = Type.UNKNOWN; 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("Non-coding_Transcript")) { classification = Classification.Noncoding_transcript; return; }
if ( s.equals("Missense") || s.equals("Missense_Mutation") ) { classification = Classification.Missense ; 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("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("miRNA") ) { classification = Classification.miRNA ; return; }
if ( s.equals("Frame_Shift_Ins") ) { classification = Classification.Frameshift ; return; } if ( s.equals("Frame_Shift_Ins") ) { classification = Classification.Frameshift ; return; }
if ( s.equals("Frame_Shift_Del") ) { 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_Ins") ) { classification = Classification.Inframe ; return; }
if ( s.equals("In_Frame_Del") ) { 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("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_Del") ) { classification = Classification.Splice_site ; return; }
if ( s.equals("Splice_Site_Ins") ) { classification = Classification.Splice_site_insertion ; 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("Promoter") ) { classification = Classification.Promoter ; return; }
if ( s.equals("De_novo_Start") ) { classification = Classification.De_novo_start ; return; } if ( s.equals("De_novo_Start") ) { classification = Classification.De_novo_start ; return; }
if ( s.equals("TX-REF-MISMATCH") ) { classification = Classification.Unclassified ; return; } if ( s.equals("TX-REF-MISMATCH") ) { classification = Classification.Unclassified ; return; }