[Biojava-l] problem reading GFF

[Schreiber, Mark]

Hi -

I have used the GenBankToGFF demo to generate GFF files for some genbank
genome files (U00096) and (AB001339). When reading these files back in I
get the following exception

java.lang.StringIndexOutOfBoundsException: String index out of range: -2
at java.lang.String.substring(String.java:1503) 	at
org.biojava.bio.program.gff.GFFParser.parseAttribute(GFFParser.java:275)
at
org.biojava.bio.program.gff.GFFParser.createRecord(GFFParser.java:230)
at org.biojava.bio.program.gff.GFFParser.parse(GFFParser.java:128)
at org.biojava.bio.program.gff.GFFParser.parse(GFFParser.java:76)

The offending line of code seems to be in the following, some how the
quote index has become -2.

} while(quoteIndx != -1 && attValList.charAt(quoteIndx-1) == '\\');
			valList.add(attValList.substring(1, quoteIndx));
			

Perhaps the while statement should begin

while(quoteInx > -1 && ...

But I might be wrong.

The same error occurs for both gbk files


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 

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