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Added new query: isMNP(feature); returns true if dbsnp feature is multi-nucleotide polymorfism (e.g. a di-nuc TA ->CC) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3806 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2010-07-16 15:32:10 +00:00
parent 74f705d943
commit 1dd8a28a5d
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
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@ -50,6 +50,10 @@ public class DbSNPHelper {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
public static boolean isMNP(DbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
public static String toMediumString(DbSNPFeature feature) {
String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved()));
if (isSNP(feature)) s += ":SNP";