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14:28 < balin> deafferret, I only posted about add_seq to bioperl-l. Should I
               start a new thread for write_aln or can I reuse this one?
14:28 <@deafferret> If it's a seperate issue I'd post a separate email
14:29 <@deafferret> ticket 2793 is definately add_seq only
14:29 < balin> I thought so too #bioperl 20090319
oh... maybe I can patch it before they do
   --jhannah 20090320

7 email discussion:
   --jhannah 20090320

12:26 < balin> deafferret, I found that add_seq function does not insert a new sequence into alignment, but replaces the old sequence. So this statement
               seems to work:
12:27 < balin> $aln->get_seq_by_pos($i)->display_id("new header");
12:27 < balin> $aln->add_seq($aln->get_seq_by_pos($i),$i-1);
12:29 <@deafferret> ahh... congrats.  :)
12:30 < balin> still, this looks awkward
12:38 < balin> It turns out I need $i-1 here because get_seq_by_pos counts from 1 and add_seq counts from 0. Would that be considered a bug?
13:01 <@deafferret> hmm... maybe a bug that can't be fixed because no one wants to break backwards-compatibility ... so a FEATURE?  :)
13:01 <@deafferret> you should probably post that to bioperl-l and ask the long white beards
13:37 < balin> yes, I'll probably do that
13:37 < balin> white beards, haha
13:46 <@deafferret> :) #bioperl 20090319

Possible bug report from #bioperl balin
   --jhannah 20090318