From ff6d28e672fca61bf5795751783f9ad57c36d654 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 30 Jan 2013 15:20:42 +0000
Subject: [PATCH] ignore sequence-region lines that cannot be parsed
---
.../artemis/io/IndexedGFFDocumentEntry.java | 24 +++++++++++++++----
1 file changed, 19 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java b/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
index b9d517959..8b5f9fe49 100644
--- a/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
@@ -106,15 +106,24 @@ public class IndexedGFFDocumentEntry implements DocumentEntry
int cnt = 0;
while( (ln = in.readLine()) != null && ln.startsWith("#"))
{
+ // ##sequence-region seqid start end
if(ln.startsWith("##sequence-region "))
{
logger4j.debug(ln);
final String parts[] = ln.split(" ");
- //sequenceNames[cnt++] = parts[1];
- contigHash.put(parts[1], new IndexContig(parts[1], 1, Integer.parseInt(parts[3]), offset));
- offset+=Integer.parseInt(parts[3]);
- cnt++;
+ try
+ {
+ contigHash.put(parts[1], new IndexContig(parts[1], 1, Integer.parseInt(parts[3]), offset));
+ offset+=Integer.parseInt(parts[3]);
+ cnt++;
+ }
+ catch(Exception ae)
+ {
+ contigHash.clear();
+ cnt = 0;
+ break;
+ }
}
}
in.close();
@@ -289,7 +298,12 @@ public class IndexedGFFDocumentEntry implements DocumentEntry
if(!combinedReference)
{
if(contig != null)
- list.add(contigHash.get(contig));
+ {
+ if(contigHash.get(contig) == null)
+ System.err.println(contig+" not found in "+this.getName());
+ else
+ list.add(contigHash.get(contig));
+ }
else
list.add(contigHash.get(sequenceNames[0]));
return list;
--
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