[Biojava-l] OutOfMemoryError with huge sequence flatfile

[Benjamin Schuster-Boeckler]

I'm trying to create a das service for a complete genome using the
dazzle servlet. The underlying sequences are stored in plain flatfiles
of about 200M each. Now unfortunately dazzle requires a Sequence object
of every contig that corresponds to an entry point. If I try to read in
one of the files into a String or directly with DNATools.readFastaDNA, I
get an OutOfMemoryError, or if I push the max. heap size I get a
java.nio.BufferOverflowException in String. How could I represent such
large Sequences without the necessity to store them in memory?

Any comment is greatly appreciated, best regards,

Benjamin Schuster-Böckler