[Biojava-l] Error writing large Fasta seqs?

[Schreiber, Mark]

Hi,

I have been getting IndexOutOfBoundsException errors when writing a
SequenceDB of large sequences to a fasta file. I added some diagnostics to
the IndexOutOfBoundsException call in the AbstractSymbolList$SubList.subStr
and I get the stack trace below.

for some unknown reason FastaFormat is calling a subList method using an end
value less than the start. It looks like it might be tied up with an error
in the SubList of the AbstractSymbolList. Is there a limit on the maximum
size for a sequence.

This error doesn't always occur, just on large sequences (sometimes)

java.lang.IndexOutOfBoundsException: Start = 67381 End = 67380 this.start =
10001 this.end = 77380 	at
org.biojava.bio.symbol.AbstractSymbolList$SubList.subStr(AbstractSymbolList.
java:212) 	at
org.biojava.bio.seq.impl.SimpleSequence.subStr(SimpleSequence.java:82) 	at
org.biojava.bio.seq.io.FastaFormat.writeSequence(FastaFormat.java:187) 	at
org.biojava.bio.seq.io.StreamWriter.writeStream(StreamWriter.java:63)


Can anyone help??

Mark