From f1a41e12f9b84b2eccd7ce76462bfc4119da8f2d Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 5 Jan 2012 12:50:05 +0000
Subject: [PATCH] changes to VCFRecord.parse()
---
.../artemis/components/variant/AbstractVCFReader.java | 8 ++++++--
uk/ac/sanger/artemis/components/variant/GraphPanel.java | 2 +-
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
index b2888ef46..41402dd80 100644
--- a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
@@ -94,7 +94,7 @@ public abstract class AbstractVCFReader
tabixIterator = null;
return null;
}
- record = VCFRecord.parse(s);
+ record = VCFRecord.parse(s, getNumberOfSamples());
if(record == null)
tabixIterator = null;
@@ -173,6 +173,7 @@ public abstract class AbstractVCFReader
final TabixReader tr = new TabixReader(vcfFileName);
String line;
boolean headerEnd = true;
+ final StringBuffer buffHeader = new StringBuffer();
while ((line = tr.readLine()) != null)
{
@@ -180,6 +181,7 @@ public abstract class AbstractVCFReader
{
if(!line.startsWith("##FILTER"))
writer.write(line+'\n');
+ buffHeader.append(line+'\n');
continue;
}
else if(headerEnd)
@@ -191,10 +193,12 @@ public abstract class AbstractVCFReader
if(line.startsWith("#"))
{
writer.write(line+'\n');
+ buffHeader.append(line+'\n');
+ tr.setHeader(buffHeader.toString());
continue;
}
- VCFRecord record = VCFRecord.parse(line);
+ VCFRecord record = VCFRecord.parse(line, tr.getNumberOfSamples());
int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
VCFFilter.setFilterString(record, vcfView, basePosition, features, tr);
writer.write(record.toString()+'\n');
diff --git a/uk/ac/sanger/artemis/components/variant/GraphPanel.java b/uk/ac/sanger/artemis/components/variant/GraphPanel.java
index 8b40d6a3e..0b321dd01 100644
--- a/uk/ac/sanger/artemis/components/variant/GraphPanel.java
+++ b/uk/ac/sanger/artemis/components/variant/GraphPanel.java
@@ -213,7 +213,7 @@ public class GraphPanel extends JPanel
String s;
while ((s = iter.next()) != null)
{
- VCFRecord record = VCFRecord.parse(s);
+ VCFRecord record = VCFRecord.parse(s, reader.getNumberOfSamples());
max = calc(record, features, reader, windowSize, nBins, snpCount, max);
}
}
--
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