Leon Timmermans

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.