From d54c272c59cbef1031a6e1f3a63c64d877b91dfd Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 12 May 2011 10:26:58 +0000
Subject: [PATCH] use filter when calculating overview
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16075 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/variant/IOUtils.java | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index d88ff3093..f7f1d45e7 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -684,7 +684,7 @@ class IOUtils
VCFRecord record;
while ((record = reader.getNextRecord(vcfView.getChr(), thisStart, thisEnd)) != null)
- count(record, count, features, reader);
+ count(record, count, features, reader, vcfView);
}
}
}
@@ -692,7 +692,7 @@ class IOUtils
{
VCFRecord record;
while ((record = reader.getNextRecord(vcfView.getChr(), sbeg, send)) != null)
- count(record, count, features, reader);
+ count(record, count, features, reader, vcfView);
}
}
@@ -711,8 +711,12 @@ class IOUtils
tab.setIntegerRowSorter(i);
}
- private static void count(VCFRecord record, int count[], FeatureVector features, AbstractVCFReader reader)
+ private static void count(VCFRecord record, int count[], FeatureVector features, AbstractVCFReader reader, VCFview vcfView)
{
+ int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
+ if(!vcfView.showVariant(record, features, basePosition, reader.isVcf_v4()) )
+ return;
+
if(record.getAlt().isNonVariant())
{
count[1]++;
--
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