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Commit 09c8d323 authored by tjc's avatar tjc
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catch NullPointerException from TabixReader

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15721 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 7ce1e92a
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...@@ -234,7 +234,7 @@ class IOUtils ...@@ -234,7 +234,7 @@ class IOUtils
{ {
e.printStackTrace(); e.printStackTrace();
} }
if(!view) if(!view)
new MessageDialog (null, "Saved Files", fastaFiles, false); new MessageDialog (null, "Saved Files", fastaFiles, false);
else else
...@@ -565,15 +565,22 @@ class IOUtils ...@@ -565,15 +565,22 @@ class IOUtils
} }
else else
{ {
TabixReader.Iterator iter = try
(((TabixReader) reader).query(chr+":"+sbeg+"-"+send)); // get the iterator
String s;
while ((s = iter.next()) != null)
{ {
VCFRecord record = VCFRecord.parse(s); TabixReader.Iterator iter =
int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom()); (((TabixReader) reader).query(chr+":"+sbeg+"-"+send)); // get the iterator
if(vcfView.showVariant(record, features, basePosition, vcf_v4) ) String s;
basesStr = getSeqsVariation(record, basesStr, sbeg, isFwd, vcf_v4); while (iter != null && (s = iter.next()) != null)
{
VCFRecord record = VCFRecord.parse(s);
int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
if(vcfView.showVariant(record, features, basePosition, vcf_v4) )
basesStr = getSeqsVariation(record, basesStr, sbeg, isFwd, vcf_v4);
}
}
catch(NullPointerException e)
{
System.err.println(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
} }
} }
return basesStr; return basesStr;
......
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