Recoder output update

[Henrikki Almusa]

Hello,

I'm updating recoder output to conform into emboss formats, using table. Now 
there seems to be no hitches and it seems to work fine. I also added an 
option to use complement strand (it used to be automatical) and put it by 
default to be no. However there is a few questions i want to check.

1. As far as i could understand recoder doesn't reverse complement the 'AjPSeq 
seq' element (in main) but uses strings copied out of it. Will this cause any 
problems with report, as report wants a sequence when it is used (even though 
at the moment, it doesn't show any bits from sequence it self). Would it 
better if sequence objects sequence is reverse complemented as well?

2. Recoder used to print the sequences (0-4) into the result file. As this 
doens't suit well with report (could use tail, don't know which would be 
better), i changed it to print sequences into extra file. However since i 
couldn't manage to make proper changes into acd file, it now creates the 
sequence file even if it would be empty. It should depend from options 
'-sshow' and '-tshow'.

I would like to be pointed into right directions with these. Patch is 
attached.
Thanks.
-- 
Henrikki Almusa
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