From 4441ba863e6c5945c6eec650a0f44580d5472a6f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 17 Feb 2011 10:45:20 +0000
Subject: [PATCH] fix in getNumberOfDeletions()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15551 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/VCFRecord.java | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 23a296b77..241f11846 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -508,7 +508,11 @@ class VCFRecord
{
String alt = getAlt().toString();
if(vcf_v4)
+ {
+ if(alt.equals("."))
+ return getRef().length();
return getRef().length()-alt.length();
+ }
int index = alt.indexOf("D");
int ndel = 0;
--
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