From edeac26ab88cd709fff1bb5c10535c2d156e82d7 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 1 Dec 2011 08:48:44 +0000
Subject: [PATCH] speed up
---
uk/ac/sanger/artemis/components/variant/VariantBase.java | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VariantBase.java b/uk/ac/sanger/artemis/components/variant/VariantBase.java
index 787c191dc..4a384f1ef 100644
--- a/uk/ac/sanger/artemis/components/variant/VariantBase.java
+++ b/uk/ac/sanger/artemis/components/variant/VariantBase.java
@@ -1,10 +1,13 @@
package uk.ac.sanger.artemis.components.variant;
+import java.util.regex.Pattern;
+
public class VariantBase
{
private VCFRecord record;
private String alt;
+ protected static Pattern COMMA_PATTERN = Pattern.compile(",");
public VariantBase(VCFRecord record, String alt)
{
@@ -76,7 +79,8 @@ public class VariantBase
protected int getNumAlleles()
{
- return alt.split(",").length + 1;
+ return COMMA_PATTERN.split(alt).length + 1;
+ //return alt.split(",").length + 1;
}
protected int getNumberOfIndels(boolean vcf_v4)
--
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