From 055ba5b2cbb5527c87f211551f6ec7a44f57d03f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 14 Mar 2011 19:05:55 +0000
Subject: [PATCH] change visibility of iterator
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15712 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 16 +++++++---------
1 file changed, 7 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index cef1a8936..374dc5b11 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -193,16 +193,17 @@ class BCFReader extends AbstractVCFReader
private VCFRecord readVCFRecord() throws IOException
{
VCFRecord bcfRecord = new VCFRecord();
- bcfRecord.setChrom( seqNames[readInt(is)] );
+ bcfRecord.setChrom( seqNames[readInt(is)] );
bcfRecord.setPos ( readInt(is)+1 );
bcfRecord.setQuality( readFloat(is) );
-
+
int slen = readInt(is);
+
byte[] str = new byte[slen];
is.read(str);
getParts(str, bcfRecord);
-
+
if(formatPattern.matcher(bcfRecord.getFormat()).matches())
{
int n_alleles = bcfRecord.getAlt().getNumAlleles();
@@ -441,14 +442,14 @@ class BCFReader extends AbstractVCFReader
return new BCFReaderIterator(chr, sbeg, send);
}
- public class BCFReaderIterator
+ protected class BCFReaderIterator
{
private String chr;
private int sbeg;
private int send;
private int count = 0;
- public BCFReaderIterator(String chr, int sbeg, int send)
+ protected BCFReaderIterator(String chr, int sbeg, int send)
{
this.chr = chr;
this.sbeg = sbeg;
@@ -463,7 +464,6 @@ class BCFReader extends AbstractVCFReader
VCFview.logger4j.debug(chr+" NOT FOUND");
return false;
}
-
long off = queryIndex(bid, sbeg);
seek(off);
return true;
@@ -509,14 +509,12 @@ class BCFReader extends AbstractVCFReader
VCFRecord bcfRecord;
while( (bcfRecord = reader.nextRecord(chr, sbeg, send)) != null )
{
- System.out.println(bcfRecord.getChrom());
if(chr != null && bcfRecord.getChrom().equals(chr))
System.out.println(bcfRecord.toString());
else
break;
}
-
-
+
reader.close();
}
catch (IOException e)
--
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