From 1dd8a28a5d7fc17d7e4c549f98e9543c48076777 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 16 Jul 2010 15:32:10 +0000 Subject: [PATCH] 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 --- .../sting/gatk/refdata/utils/helpers/DbSNPHelper.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java index cc9374c0b..fec625b40 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java @@ -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";