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, <
[email protected]>
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
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
