From a960f1cd90d7986a3f7a9062ece5756cadc60fec Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 14 Dec 2011 13:49:30 +0000
Subject: [PATCH] speed up
---
.../artemis/components/variant/VCFFilter.java | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index efd4b750e..019ef994f 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -58,6 +58,7 @@ public class VCFFilter extends JFrame
{
private static final long serialVersionUID = 1L;
+ private static boolean useHeader = true;
private static int MIN_DP = 0;
private static float MIN_MQ = 0;
private static float MIN_AF1 = 0;
@@ -258,6 +259,7 @@ public class VCFFilter extends JFrame
if(info.size() == 0)
{
+ useHeader = false;
// min DP
c.gridy = c.gridy+1;
c.gridx = 0;
@@ -494,7 +496,7 @@ public class VCFFilter extends JFrame
}
}
- if(FilteredPanel.getFilters().size() > 0)
+ if(useHeader)
{
Hashtable<String, RecordFilter> filters = FilteredPanel.getFilters();
@@ -530,9 +532,12 @@ public class VCFFilter extends JFrame
return false;
continue;
}
- else if( record.getInfoValue(id) == null ||
- !recFilter.pass(record, record.getInfoValue(id).split(","), vcfReader))
- return false;
+ else
+ {
+ String inf = record.getInfoValue(id);
+ if(inf == null || !recFilter.pass(record, inf.split(","), vcfReader))
+ return false;
+ }
break;
case HeaderLine.FORMAT_LINE: // FORMAT Genotype line
String samples[] = record.getFormatValues(id);
--
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