[Biojava-l] BufferedReader and FastaFormat

[Schreiber, Mark]

Hi -

When working with small FASTA libraries (in terms of the number of
entries) the following snippet of code works fine,
        try{
          SequenceIterator i = SeqIOTools.readFastaDNA(new
BufferedReader(new FileReader(f)));
          while(i.hasNext()){
            Sequence s = i.nextSequence();
            db.addSequence(s);
          }catch(...... More code here.......


However when reading a FASTA library of approx 15600 sequences the
following exception is thrown.

java.io.IOException: Mark invalid
	at java.io.BufferedReader.reset(BufferedReader.java:467)
	at
org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:164
)
	at
org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:121)
	at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100)
rethrown as org.biojava.bio.BioException: Could not read sequence
	at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103)

When I increase the buffer size of the buffered reader to 6096 (an
arbitrarily chosen figure) the parsing seems to go fine. It seems like
this may be a potential flaw in the FastaFormat somewhere around here:

		if (parseStart < bytesRead && cache[parseStart] == '>')
{
		    r.reset();
		    if (r.skip(parseStart) != parseStart)
			throw new IOException("Couldn't reset to start
of next sequence");
		    reachedEnd = true;
		}

Notably the  if (r.skip(parseStart) != parseStart) can't even be reached
as r.reset() will spit the dummy first. Although a conveluted try catch
chain can keep on increasing the buffer size until a file is read this
is a bit of a pain and knowing in advance the required buffer size is
not always possible.

Any ideas on how to fix this problem?

Mark
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