From 528af603ea0255914975cda45ae2fb347dc5dcdf Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Sat, 4 Dec 2010 12:48:32 +0000
Subject: [PATCH] use getNumAlleles()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15168 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/BCFReader.java | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index 67ae68adb..03e91955f 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -181,8 +181,10 @@ class BCFReader
getParts(str, bcfRecord);
if(formatPattern.matcher(bcfRecord.format).matches())
- {
- int nc = 3;
+ {
+ int n_alleles = bcfRecord.getNumAlleles();
+ int nc = (int) (n_alleles * ((float)(((float)n_alleles+1.f)/2.f)));
+
if(bcfRecord.alt.equals("."))
nc = 1;
--
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