Error parsing FASTA in multiple passes

@andreasprlic

Dak reported the following bug on the mailing list:

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.

@andreasprlic created a branch, https://github.com/biojava/biojava/tree/DakFastaHeader which contains the failing TestFASTAReader.

Looks like a bug introduced a long time ago by #282

Attempt to fix issue biojava#659 - Error parsing FASTA in multiple pa…

Created pull request #687

Merge pull request #687 from arojnuckarin/issue-659

Was this completely fixed by #687?

I recently pulled biojava-core 4.2.9 from maven repo and it looks like this particular bug is still there.
I was thinking that the since the pull request has been merged, the fix should propagate into maven sooner or later, but it looks like that's not the case.

Is there something that need to take place before the change can go into the 4.2.x official release? Anything that I need to do?

Thanks,
dak

The pull request went into the master branch only and not into the bugfixes-4.2 branch. The fix is already in the 5.0.0-alpha13 release and it will be there also when the final 5.0.0 goes out.

If you want the fix in the next 4.2.x release, you will need to make a separate pull request for that. You will just need to cherry-pick the appropriate commits. Thanks!

Do we have an estimate as to when 5.0.0 will go out and how much work is likely involved in upgrading from the code that uses 4.2.x to 5.0? Thanks again for your help, dak From: Jose Manuel Duarte [mailto:notifications@github.com] Sent: Wednesday, November 29, 2017 7:26 PM To: biojava/biojava <biojava@noreply.github.com> Cc: Rojnuckarin, Dak <atipatr@amgen.com>; Comment <comment@noreply.github.com> Subject: Re: [biojava/biojava] Error parsing FASTA in multiple passes (#659) The pull request went into the master branch only and not into the bugfixes-4.2 branch. The fix is already in the 5.0.0-alpha13 release and it will be there also when the final 5.0.0 goes out. If you want the fix in the next 4.2.x release, you will need to make a separate pull request for that. You will just need to cherry-pick the appropriate commits. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_biojava_biojava_issues_659-23issuecomment-2D348042233&d=DwMFaQ&c=Sexio4usKrYWFsrnxgjbcQ&r=BN3CILveVUlvYrOz3uojdjSCqImtuPxs4gsh43cQxOQ&m=yA_nIkBuCZ9inINuytG-eMaZJD6RlHbIv-MzZYtORUk&s=DXUbhU7IrdxlN_OfTJGWnZP4HYis0Ku9XmGBdWqQTg4&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AGzItNfP4-5FLETjuCbRyd8GQqYiyA09TZks5s7fYNgaJpZM4NJAoN&d=DwMFaQ&c=Sexio4usKrYWFsrnxgjbcQ&r=BN3CILveVUlvYrOz3uojdjSCqImtuPxs4gsh43cQxOQ&m=yA_nIkBuCZ9inINuytG-eMaZJD6RlHbIv-MzZYtORUk&s=pQvMpnYKBZZ4E4Za1y6QCZywfANJzQ6wXZI7mrelc6U&e=>.

The intention is to release 5.0.0 early next year. Most changes are in the structure module, adapting code that uses the structure module can require some work. For other modules the changes are much less dramatic.

Attempt to fix issue #659 - Error parsing FASTA in multiple passes

@arojnuckarin

@arojnuckarin I've just cherry-picked your fix into the bugfixes-4.2 branch. I'm going to release a new bugfix version in the next days.

Reading the above, it looks that this is fixed. Closing. If you know otherwise please reopen.

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Error parsing FASTA in multiple passes #659

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Error parsing FASTA in multiple passes #659

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psoares commented on Jun 2, 2017

arojnuckarin commented on Jul 8, 2017

lafita commented on Aug 10, 2017

arojnuckarin commented on Nov 29, 2017

josemduarte commented on Nov 30, 2017

arojnuckarin commented on Nov 30, 2017

josemduarte commented on Nov 30, 2017

josemduarte commented on Dec 12, 2017

josemduarte commented on Mar 7, 2018

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