From a536813c739993bcf230dd4e9e6f3ab6fb39ee4b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 30 Nov 2010 11:07:42 +0000
Subject: [PATCH] test for BCF file format
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15132 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/VCFview.java | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index e27a8534f..7d679d162 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -604,11 +604,20 @@ public class VCFview extends JPanel
buff.append(fileName+"\n");
try
{
- FileInputStream fileStream = new FileInputStream(fileName);
- BlockCompressedInputStream inputStrean = new BlockCompressedInputStream(fileStream);
+ if(IOUtils.isBCF(fileName))
+ {
+ JOptionPane.showMessageDialog(null,
+ "Looks like a BCF formated file.\n"+
+ "Convert to VCF and use bgzip and tabix\n"+
+ "to compress and index respectively.",
+ "Unsupported Format",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ BlockCompressedInputStream is =
+ new BlockCompressedInputStream(new FileInputStream(fileName));
String line;
- while( (line = TabixReader.readLine(inputStrean) ) != null )
+ while( (line = TabixReader.readLine(is) ) != null )
{
if(!line.startsWith("##"))
break;
@@ -1495,7 +1504,7 @@ public class VCFview extends JPanel
System.setProperty("default_directory", System.getProperty("user.dir"));
FileSelectionDialog fileSelection = new FileSelectionDialog(
null, true, "VCFview", "VCF");
- vcfFileList = fileSelection.getFiles(".vcf");
+ vcfFileList = fileSelection.getFiles(".*\\.[bv]{1}cf(\\.gz)*$");
reference = fileSelection.getReferenceFile();
if(reference.equals(""))
reference = null;
--
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