From e23f8c58383c812acce47b1fad1adf1694ac85e5 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 16 Mar 2011 11:08:55 +0000
Subject: [PATCH] fix for insertion
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15729 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/IOUtils.java | 3 +++
1 file changed, 3 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 2c2bcdc3f..8d89c0b62 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -680,7 +680,10 @@ class IOUtils
buff.append("-");
}
else if(vcfRecord.getAlt().isInsertion(vcf_v4))
+ {
buff.append(getBase(vcfRecord.getAlt().toString(), isFwd));
+ position+=(vcfRecord.getRef().toString().length()-1);
+ }
else if(vcfRecord.getAlt().isMultiAllele())
{
String base = MultipleAlleleVariant.getIUBCode(vcfRecord);
--
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