From 426f0590c2787b3eea665d8d98cdf74c83241dee Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 21 Feb 2011 12:18:24 +0000
Subject: [PATCH] use getNumberofIndels()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15571 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/IOUtils.java | 2 +-
uk/ac/sanger/artemis/components/variant/VariantBase.java | 6 ++++--
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 3486fde53..ddae3a9cc 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -390,7 +390,7 @@ class IOUtils
if(vcfRecord.getAlt().isDeletion(vcf_v4))
{
- int ndel = vcfRecord.getAlt().getNumberOfDeletions(vcf_v4);
+ int ndel = vcfRecord.getAlt().getNumberOfIndels(vcf_v4);
if(!vcfRecord.getAlt().toString().equals(".") && isFwd)
{
buff.append(getBase(vcfRecord.getAlt().toString(), isFwd));
diff --git a/uk/ac/sanger/artemis/components/variant/VariantBase.java b/uk/ac/sanger/artemis/components/variant/VariantBase.java
index aeedb74d4..f15111408 100644
--- a/uk/ac/sanger/artemis/components/variant/VariantBase.java
+++ b/uk/ac/sanger/artemis/components/variant/VariantBase.java
@@ -79,16 +79,18 @@ public class VariantBase
return alt.split(",").length + 1;
}
- protected int getNumberOfDeletions(boolean vcf_v4)
+ protected int getNumberOfIndels(boolean vcf_v4)
{
if (vcf_v4)
{
if (alt.equals("."))
return record.getRef().length();
- return record.getRef().length() - alt.length();
+ return Math.abs(record.getRef().length() - alt.length());
}
int index = alt.indexOf("D");
+ if(index < 0)
+ index = alt.indexOf("I");
int ndel = 0;
try
{
--
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