From 835bfe5f8db6ebcfbe3e6803b8cae636a39905e2 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 20 Dec 2011 16:14:14 +0000
Subject: [PATCH] fix for writing filter lines in VCF header
---
.../artemis/components/variant/AbstractVCFReader.java | 7 ++++---
uk/ac/sanger/artemis/components/variant/FilteredPanel.java | 6 +++++-
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
index 88e7f79de..b2888ef46 100644
--- a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
@@ -170,9 +170,10 @@ public abstract class AbstractVCFReader
return;
}
- TabixReader tr = new TabixReader(vcfFileName);
+ final TabixReader tr = new TabixReader(vcfFileName);
String line;
boolean headerEnd = true;
+
while ((line = tr.readLine()) != null)
{
if(line.startsWith("##"))
@@ -183,7 +184,7 @@ public abstract class AbstractVCFReader
}
else if(headerEnd)
{
- writer.write(FilteredPanel.getHeader()+"\n");
+ writer.write(FilteredPanel.getHeader());
headerEnd = false;
}
@@ -220,7 +221,7 @@ public abstract class AbstractVCFReader
{
if(str.startsWith("#CHROM"))
{
- buff.append(filterLines+"\n");
+ buff.append(filterLines);
buff.append(str+"\n");
}
else
diff --git a/uk/ac/sanger/artemis/components/variant/FilteredPanel.java b/uk/ac/sanger/artemis/components/variant/FilteredPanel.java
index 5f0d81952..967e4a85d 100644
--- a/uk/ac/sanger/artemis/components/variant/FilteredPanel.java
+++ b/uk/ac/sanger/artemis/components/variant/FilteredPanel.java
@@ -169,7 +169,11 @@ import javax.swing.border.Border;
while(filterStr.hasMoreElements())
{
RecordFilter recFilter = filters.get(filterStr.nextElement());
- buff.append(recFilter.getHeaderLine().toString());
+ buff.append("##FILTER=<ID=");
+ buff.append(recFilter.getHeaderLine().getID());
+ buff.append(",Description=\"");
+ buff.append(recFilter.toString());
+ buff.append("\">\n");
}
return buff.toString();
}
--
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