From 0a4ea0040e0ccc460386524e8244bffad65ebe78 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 20 Dec 2011 16:41:40 +0000
Subject: [PATCH] fix for writing out VCF filter column
---
uk/ac/sanger/artemis/components/variant/VCFFilter.java | 3 ++-
uk/ac/sanger/artemis/components/variant/VCFRecord.java | 4 +++-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index e1a06ee2d..46dca2bb0 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -751,7 +751,8 @@ public class VCFFilter extends JFrame
}
}
- if(record.getFilter().length() == 0)
+ if( record.getFilter().length() == 0 ||
+ (record.getFilter().length() == 1 && record.getFilter().equals(".")) )
record.setFilter("PASS");
return;
}
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 6cb838fba..cee36ab28 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -312,7 +312,9 @@ public class VCFRecord
protected void appendFilter(String filter)
{
- if(getFilter().length() == 0 || (getFilter().length() == 1 && getFilter().equals(".")))
+ if( getFilter().length() == 0 ||
+ (getFilter().length() == 1 && getFilter().equals(".")) ||
+ (getFilter().length() == 3 && getFilter().equals("PASS")))
this.filter = filter;
else
this.filter += ";" + filter;
--
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