Erik Aronesty > Bio-IlluminaSAV-1.0.9706 > Bio::IlluminaSAV

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Module Version: 1.0.9706   Source  

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
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