[Biojava-l] Issue with FASTA reader

[Rojnuckarin, Dak]

Hello,

Andreas mentioned he created a branch in github to contain my test code:

https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e21684605cf2f7b

but I have not heard back in a while.

What’s the process/etiquette of getting involved and attempt the fix myself?

Thanks,
dak

From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: Wednesday, April 19, 2017 4:34 PM
To: Rojnuckarin, Dak <atipatr at amgen.com>
Cc: biojava-l at mailman.open-bio.org
Subject: Re: [Biojava-l] Issue with FASTA reader

Thanks, Dak. I'll create a branch in git which will contain your test, then we can take it from there.

Andreas



On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <atipatr at amgen.com<mailto:atipatr at amgen.com>> wrote:
Hi,

I have a FASTA file that contain one sequence. I initialized FASTA reader as described in the tutorial, called process() and get one record as expected. However, if I re-initialized another FASTA reader opening the same one-record file, called process(1) and null is returned. If I tried to read two-record FASTA file, the first process(1) works, but not the second call to process(1) return null. Based on a superficial glance, it looks like the if statement at line 194 of FastaReader.java may be the culprit.

Test code attached.

Thanks,
Dak Rojnuckarin
Research Informatics
Amgen



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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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