<div dir="ltr">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. <div><br></div><div>See <a href="https://help.github.com/articles/creating-a-pull-request-from-a-fork/">https://help.github.com/articles/creating-a-pull-request-from-a-fork/</a> for more info</div><div><br></div><div>Jose</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 7, 2017 at 4:27 PM, Rojnuckarin, Dak <span dir="ltr"><<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">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: <a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>). If not, I would appreciate any help figuring this out.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">dak<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Jose Duarte [mailto:<a href="mailto:jose.duarte@rcsb.org" target="_blank">jose.duarte@rcsb.org</a>]
<br>
<b>Sent:</b> Thursday, June 1, 2017 10:37 AM<br>
<b>To:</b> Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>><br>
<b>Cc:</b> Andreas Prlic <<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>>; <a href="mailto:biojava-l@mailman.open-bio.org" target="_blank">biojava-l@mailman.open-bio.org</a></span></p><div><div class="h5"><br>
<b>Subject:</b> Re: [Biojava-l] Issue with FASTA reader<u></u><u></u></div></div><p></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Dear Dak<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">All the best<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Jose<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hello,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Andreas mentioned he created a branch in github to contain my test code:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><a href="https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e21684605cf2f7b" target="_blank">https://github.com/biojava/<wbr>biojava/commit/<wbr>9de8e3633a8d66fc4050f14b2e2168<wbr>4605cf2f7b</a><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">but I have not heard back in a while.
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">What’s the process/etiquette of getting involved and attempt the fix myself?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Thanks,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">dak</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
<a href="mailto:andreas.prlic@gmail.com" target="_blank">andreas.prlic@gmail.com</a> [mailto:<a href="mailto:andreas.prlic@gmail.com" target="_blank">andreas.prlic@gmail.<wbr>com</a>]
<b>On Behalf Of </b>Andreas Prlic<br>
<b>Sent:</b> Wednesday, April 19, 2017 4:34 PM<br>
<b>To:</b> Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>><br>
<b>Cc:</b> <a href="mailto:biojava-l@mailman.open-bio.org" target="_blank">biojava-l@mailman.open-bio.org</a><br>
<b>Subject:</b> Re: [Biojava-l] Issue with FASTA reader</span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Thanks, Dak. I'll create a branch in git which will contain your test, then we can take it from there.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Andreas<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Test code attached.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
<p class="MsoNormal">Dak Rojnuckarin<u></u><u></u></p>
<p class="MsoNormal">Research Informatics<u></u><u></u></p>
<p class="MsoNormal">Amgen<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><br>
______________________________<wbr>_________________<br>
Biojava-l mailing list - <a href="mailto:Biojava-l@mailman.open-bio.org" target="_blank">
Biojava-l@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" target="_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biojava-l</a><u></u><u></u></p>
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<p class="MsoNormal"><br>
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<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">--
<u></u><u></u></p>
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<p class="MsoNormal">------------------------------<wbr>------------------------------<wbr>-----------<br>
Dr. Andreas Prlic<br>
RCSB PDB Protein Data Bank<u></u><u></u></p>
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<p class="MsoNormal">Technical & Scientific Team Lead<u></u><u></u></p>
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<p class="MsoNormal">University of California, San Diego<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Editor Software Section <u></u><u></u></p>
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<p class="MsoNormal">PLOS Computational Biology<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">BioJava Project Lead<br>
------------------------------<wbr>------------------------------<wbr>-----------<u></u><u></u></p>
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______________________________<wbr>_________________<br>
Biojava-l mailing list - <a href="mailto:Biojava-l@mailman.open-bio.org" target="_blank">Biojava-l@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" target="_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biojava-l</a><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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