NAME
Bio::SFF::Entry - An SFF entry
VERSION
version 0.007
SYNOPSIS
while(my $entry = $reader->next_entry) {
say '>', $entry->name;
say $entry->bases;
}DESCRIPTION
This object represents an entry in an SFF file. It contains both processed data (the nucleotides and quality scores) and raw data (e.g. flowgram values).
ATTRIBUTES
name
The name of this sequence
bases
The nucleotides of this sequence
flowgram_values
Returns an array containing all flowgram values.
flow_index_per_base
This contains the flow positions for each base in the called sequence (i.e., for each base, the position in the flowgram whose estimate resulted in that base being called). These values are "incremental" values, meaning that the stored position is the offset from the previous flow index in the field. All position values (prior to their incremental encoding) use 1-based indexing, so the first flow is flow 1.
quality_scores
The quality scores for each of the bases in the sequence, where the values use the standard -log10 probability scale.
clip_qual_left
The first base after the clipping point for quality, using 1-based indexing.
clip_qual_right
The last base before the clipping point for quality, using 1-based indexing.
clip_adaptor_left
The first base after the clipping point for quality, using 1-based indexing.
clip_adaptor_right
The last base before the clipping point for quality, using 1-based indexing.
AUTHOR
Leon Timmermans <leont@cpan.org>
COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Leon Timmermans, Utrecht University.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.