#6 ArrayIndexOutOfBoundsException, seed out of ref seq bounds?

[Ntino]

I am getting ArrayIndexOutOfBoundsException when - in my opinion -
a seed of length 3 for example, tries to match the reference sequence
at the second to last position.

The problem comes from the DNAString class (1st in the error stack pasted below)
where seeds with repetitive sequences are examined, and the loop at method
DNAString.repseed in line 254 of this class, examines seeds with identical nucleotides
along their length.

The MerReduce (2nd in the err stack below) is the calling class of the DNAString.repseed method,
at line 140. A change in line 140 of MerReduce to check if the current sequence position + the seed
length don't add up to over the sequence length, would solve the ArrayIndexOutOfBoundsException
error.

java.lang.ArrayIndexOutOfBoundsException: 42358
at cloudBurst.DNAString.repseed(Unknown Source)
at cloudBurst.MerReduce$MapClass.map(Unknown Source)
at cloudBurst.MerReduce$MapClass.map(Unknown Source)
at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:47)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:227)
at org.apache.hadoop.mapred.TaskTracker$Child.main(TaskTracker.java:2210)