question about type gapany

Guy Bottu gbottu at
Thu Mar 3 18:51:03 UTC 2005

	Dear colleagues,

I just noticed a strange thing. The ACD file for emma contains :

  seqall: sequence  [
    parameter: "Y"
    type: "gapany"

I tried to replace "gapany" by "gap", so that the input sequences should 
be degapped before the alignment procedure starts. I was surprised to get 
an output file with unaligned sequences. As if the degapping was also 
performed on the output instead of just on the input. Is this normal ?
I ask the question because I have developed programs that work like emma 
an I was busy adding the "type" attributes, in order to improve them. Has 
anybody already seen such behaviour ? Or am I misunderstanding something ? 

	Guy Bottu

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