From 8e7a4bc69e7522cca95155bfc5201ae884cde63c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 3 Jan 2012 15:12:50 +0000
Subject: [PATCH] add FORMAT filters when using setFilterString()
---
.../artemis/components/variant/VCFFilter.java | 25 +++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index ada5fb9dd..76f2384c1 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -28,7 +28,6 @@ import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
-import java.awt.Insets;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -718,7 +717,29 @@ public class VCFFilter extends JFrame
!recFilter.pass(record, record.getInfoValue(id).split(","), vcfReader))
record.appendFilter(id);
break;
- case HeaderLine.FORMAT_LINE: // FORMAT
+
+ case HeaderLine.FORMAT_LINE: // FORMAT Genotype line
+ final String samples[] = record.getFormatValues(id);
+ if(samples == null)
+ {
+ record.appendFilter(id);
+ break;
+ }
+
+ //if (recFilter.getHeaderLine().isFlag())
+ //{
+ // return true;
+ //}
+
+ for(int i=0; i<samples.length; i++)
+ {
+ if( samples[i] == null || !recFilter.pass(record, samples[i].split(","), vcfReader))
+ {
+ record.appendFilter(id);
+ break;
+ }
+ }
+
break;
case HeaderLine.FILTER_LINE: // FILTER
break;
--
GitLab