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Bio::DB::GFF::Aggregator::match_gap -- GFF3 match aggregator

Bio::DB::GFF::Aggregator::match_gap(3pm) User Contributed Perl Documentation Bio::DB::GFF::Aggregator::match_gap(3pm)

NAME

Bio::DB::GFF::Aggregator::match_gap -- GFF3 match aggregator

SYNOPSIS

 -------------------------------------------------
 Aggregator method: match_gap
 Main method:       match
 Sub methods:       match
 -------------------------------------------------

DESCRIPTION

This aggregator is used for GFF3 style gapped alignments, in which there is a single feature of method 'match' with a 'Gap' attribute.
The 'Gap' attribute's format consists of a series of (operartion,length) pairs separated by space characters, for example: 'M8 D3 M6'. (see GFF reference for complete explanation)
This module only recognizes the M and D operators, which should be sufficient for simple nucleotide to nucleotide alignments.

BUGS

None reported.

SEE ALSO

Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR

Dmitri Bichko
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
2014-07-10 perl v5.18.2