There appears to be a bug in the writeSequence(Sequence seq, PrintStream os)
method of FastaFormat.java
If you have a sequence whose length is exactly divisable by the
lineWidth (60), then you get an IndexOutOfBounds exception when writing
it out.
The problem occurs at line 207:
for(int pos = 1; pos <= seq.length() + 1; pos += lineWidth) {
- removing the "+ 1" or making it "<" only eliminates the error
for example, seq length = 30000
last 2 times through the for loop for outputting gives:
start: 29941 end:30000
start: 30001 end:30000
Cheers,
Simon Foote
--
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-991-4342 [F] 613-952-9092
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