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lib/FASTX/Reader.pm  view on Meta::CPAN

our @ISA = qw(Exporter);

#ABSTRACT: A simple module to parse FASTA and FASTQ files, supporting compressed files and paired-ends.

use constant GZIP_SIGNATURE => pack('C3', 0x1f, 0x8b, 0x08);


sub new {
    # Instantiate object
    my $class = shift @_;
    my $self = bless {} => $class;
    my $args = {};
    
    # Named parameters: undefined $_[0] will read STDIN!
    if (defined $_[0] and substr($_[0], 0, 1) eq '-') {
      my %data = @_;
        # Try parsing
        for my $i (keys %data) {
            if ($i =~ /^-(file|filename)/i) {
                $args->{filename} = $data{$i};
            } elsif ($i =~ /^-(loadseqs)/i) {