NAME

Bio::IlluminaSAV - Parse Illumina SAV files

SYNOPSIS

Routines for parsing and extracting information from Illumina SAV files (aka "InterOp").

use IlluminaSAV;

my $savs = IlluminaSAV->new("/path/to/rundirectory");
my @qmetrics = $savs->quality_metrics();
my $cur_cycle = $savs->cur_cycle();
my $num_reads = $savs->num_reads();

DESCRIPTION

Easy access to Illumina's SAV file data.

AUTHOR

Andrew Hoerter & Erik Aronesty, <earonesty@cpan.org>

COPYRIGHT AND LICENSE

Copyright (C) 2013 Erik Aronesty / Expression Analysis

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.

CONSTANTS

# constants you can use
TILE_METRIC_CLUST_DENS
TILE_METRIC_PF_CLUST_DENS
TILE_METRIC_NUM_CLUSTERS
TILE_METRIC_NUM_PF_CLUSTERS
TILE_METRIC_CONTROL_LANE

FUNCTIONS

cur_cycle Return the current run extraction cycle

cur_copy_cycle Return the current copy cycle

max_cycles Return the maximum number of cycles

num_lanes Return the number of lanes

num_reads Return the number of reads

run_info Returns a hash with RunInfo.xml info

extraction_metrics Load extraction metrics

quality_metrics Load quality metrics

error_metrics Load error metrics

tile_metrics Load tile metrics

corrected_int_metrics Load corrected int metrics

control_metrics Load control metrics

image_metrics Load image metrics

parse_sav_file(PATHNAME) Load binary SAV-format file PATHNAME, inferring the type from the filename