[Bioperl-l] hickup in SimpleAlign remove_gaps method

Albert Vilella avilella at gmail.com
Fri Oct 13 11:26:47 EDT 2006


Hi all,

While using the remove_gaps method in Bio::SimpleAlign I found out
that if the alignment is (bad enough for) having no columns without
any gap at all, the method will give a:

Use of uninitialized value in split at this line in add_seq:

map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq);

So my idea was to tweak this line to something like:

map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq || '');

But I am unsure about any other side effects this may have.

Anyone?

    Albert.


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