Commit 60bb6794 authored by Abel Ureta-Vidal's avatar Abel Ureta-Vidal
Browse files

Added alignment_length method again for use in homologous gene pairing...

Added alignment_length method again for use in homologous gene pairing pipeline, to regenerate the original perc_id and perc_pos that blast gives. The blast Runnable returns the perc_id based on the query length without indels
parent e420be71
......@@ -190,6 +190,38 @@ sub cigar_string {
}
=head2 alignment_length
Arg [1] : None
Example :
Description: return the alignment length (including indels) based on the cigar_string
Returntype : int
Exceptions :
Caller :
=cut
sub alignment_length {
my $self = shift;
if (! defined $self->{'_alignment_length'} && defined $self->cigar_string) {
my @pieces = ( $self->cigar_string =~ /(\d*[MDI])/g );
unless (@pieces) {
print STDERR "Error parsing cigar_string\n";
}
my $alignment_length = 0;
foreach my $piece (@pieces) {
my ($length) = ( $piece =~ /^(\d*)/ );
if (! defined $length || $length eq "") {
$length = 1;
}
$alignment_length += $length;
}
$self->{'_alignment_length'} = $alignment_length;
}
return $self->{'_alignment_length'};
}
=head2 ungapped_features
......
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