[Biojava-l] Issue with FASTA reader

[Jose Duarte]

Make sure you create your own fork of biojava and then push to it. After
that you can do a pull request into the main biojava repository.

See https://help.github.com/articles/creating-a-pull-request-from-a-fork/
for more info

Jose

On Fri, Jul 7, 2017 at 4:27 PM, Rojnuckarin, Dak <atipatr at amgen.com> wrote:

> Hi,
>
>
>
> I am trying to commit my branch and got “git-receive-pack not permitted”.
> I suspect I need commit privilege for biojava repository. If so, my github
> username is arojnuckarin (email: atipatr at amgen.com). If not, I would
> appreciate any help figuring this out.
>
>
>
> Thanks,
>
> dak
>
>
>
> *From:* Jose Duarte [mailto:jose.duarte at rcsb.org]
> *Sent:* Thursday, June 1, 2017 10:37 AM
> *To:* Rojnuckarin, Dak <atipatr at amgen.com>
> *Cc:* Andreas Prlic <andreas at sdsc.edu>; biojava-l at mailman.open-bio.org
>
> *Subject:* Re: [Biojava-l] Issue with FASTA reader
>
>
>
> Dear Dak
>
>
>
> The best way of fixing it yourself is that you modify the code in your own
> github fork (ideally in a branch, not in master) and then submit a pull
> request so that your patch can be peer reviewed.
>
>
>
> All the best
>
>
>
> Jose
>
>
>
>
>
> On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <atipatr at amgen.com>
> wrote:
>
> Hello,
>
>
>
> Andreas mentioned he created a branch in github to contain my test code:
>
>
>
> https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e2168
> 4605cf2f7b
>
>
>
> 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>
> 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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> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>
> --
>
> -----------------------------------------------------------------------
> 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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>
>
>
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