[Bioperl-l] bl2seq parse nightmare

[Julio Fernandez Banet]

Hello.
I'm parsing my bl2seq seq report.
I tried with BPbl2seq and with alignIO but my problem is exactly the same in
both cases.
When I call both sequences in the alignment, I get the query sequence with
gaps on it (ie: agtc-aactggtca) but when it comes to the subject the gaps
disapear (ie: tcagttgaccagt).
This is a big problem for me as I would like to get the values in the
position where the cigar line says is a mismatch and when a gap is in the
subject is gives me the wrong values.
Please I'm completely desperate as it's the last bug I need to fix to finish
my program so any help or advice will be really wellcome.
Thanks a lot.
Julio
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