Bug #109324 for Bio-Tools-Primer3Redux: tag PRIMER_FIRST_BASE

Sat Nov 21 12:00:10 2015 Charles.Beauchamps [...] SYNGENTA.COM - Ticket created

Subject:	tag PRIMER_FIRST_BASE_INDEX partially taken in account
Date:	Sat, 21 Nov 2015 16:59:51 +0000
To:	"bug-Bio-Tools-Primer3Redux [...] rt.cpan.org" <bug-Bio-Tools-Primer3Redux [...] rt.cpan.org>
From:	Beauchamps Charles FRSS <Charles.Beauchamps [...] SYNGENTA.COM>

Hello, After searching a bit it occur to me that the Primer3 tag <PRIMER_FIRST_BASE_INDEX=1> seems to only be taken in account for the first record, as if this tag was a per-record tag when it is documented as a <GLOBAL> tag This has an impact on all returned Primers (positions are shifted by +1) Lead on where to start: cf line 275 of Primer3Redux/Result.pm Technical details: Premier3: This is primer3 (libprimer3 release 2.3.6) Module: Bio-Tools-Primer3Redux-0.09 Perl: This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi OS: Linux SMP Sun Nov 10 22:19:54 EST 2013 x86_64 GNU/Linux PS: the <Reporting Bugs> section of POD seems to be out of date (the provided link is redirecting elsewhere) Attached are primer3 input/output causing the bug to show. Charles B. Show quoted text

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Sat Sep 16 17:01:24 2017 cjfields [...] uiuc.edu - Correspondence added

I may have to check this against the latest updates for Primer3, which are now on the github repo: https://github.com/cjfields/Bio-Tools-Primer3Redux Will leave this open but will stick a github issue pointing here just in case. On Sat Nov 21 11:00:10 2015, Charles.Beauchamps@SYNGENTA.COM wrote: Show quoted text

> Hello, > > After searching a bit it occur to me that the > Primer3 tag <PRIMER_FIRST_BASE_INDEX=1> seems to only be taken in > account for the first record, as if this tag was a per-record tag when > it is documented as a <GLOBAL> tag > This has an impact on all returned Primers (positions are shifted by > +1) > > Lead on where to start: cf line 275 of Primer3Redux/Result.pm > > Technical details: > Premier3: This is primer3 (libprimer3 release 2.3.6) > Module: Bio-Tools-Primer3Redux-0.09 > Perl: This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi > OS: Linux SMP Sun Nov 10 22:19:54 EST 2013 x86_64 GNU/Linux > > PS: the <Reporting Bugs> section of POD seems to be out of date (the > provided link is redirecting elsewhere) > > Attached are primer3 input/output causing the bug to show. > > Charles B. > > ________________________________ > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and delete > the original and any copies. Any use of the message by you is > prohibited.

Sat Sep 16 17:01:25 2017 The RT System itself - Status changed from 'new' to 'open'

Bug #109324 for Bio-Tools-Primer3Redux: tag PRIMER_FIRST_BASE_INDEX partially taken in account