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Commit 055ba5b2 authored by tjc's avatar tjc
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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
parent 5d4b8d09
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......@@ -198,6 +198,7 @@ class BCFReader extends AbstractVCFReader
bcfRecord.setQuality( readFloat(is) );
int slen = readInt(is);
byte[] str = new byte[slen];
is.read(str);
......@@ -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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