From 5c5a11daf24974c102f4ba4d50b3f9f82f0f8bc4 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 1 Mar 2011 12:13:21 +0000
Subject: [PATCH] fix for finding synonymous and non-synonymous variants
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15629 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/VCFRecord.java | 13 ++++---------
1 file changed, 4 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 6a55e784c..08ce4b6e1 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -356,11 +356,9 @@ class VCFRecord
{
RangeVector ranges = feature.getLocation().getRanges();
intronlength = 0;
-
for(int j=0; j< ranges.size(); j++)
{
Range range = (Range) ranges.get(j);
-
if(j > 0)
{
if(feature.isForwardFeature())
@@ -379,16 +377,14 @@ class VCFRecord
if(feature.isForwardFeature())
{
- mod = (basePosition-feature.getRawFirstBase())%3;
- codonStart = basePosition-feature.getRawFirstBase()-mod;
+ mod = (basePosition-feature.getRawFirstBase()-intronlength)%3;
+ codonStart = basePosition-feature.getRawFirstBase()-intronlength-mod;
}
else
{
- mod = (feature.getRawLastBase()-basePosition)%3;
- codonStart = feature.getRawLastBase()-basePosition-mod;
+ mod = (feature.getRawLastBase()-basePosition-intronlength)%3;
+ codonStart = feature.getRawLastBase()-basePosition-intronlength-mod;
}
-
- codonStart-=intronlength;
try
{
@@ -397,7 +393,6 @@ class VCFRecord
char codon[] = feature.getBases().substring(codonStart,
codonStart + 3).toLowerCase().toCharArray();
- // String oldBase = new String(codon);
char aaRef = AminoAcidSequence.getCodonTranslation(codon[0],
codon[1], codon[2]);
--
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