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lib/BioX/Seq/Stream.pm  view on Meta::CPAN

use constant MAGIC_FQZC => '.fqz';
use constant MAGIC_BAM  => pack('C4', 0x42, 0x41, 0x4d, 0x01);
use constant MAGIC_2BIT => pack('C4', 0x1a, 0x41, 0x27, 0x43);
use constant MAGIC_ZSTD => pack('C4', 0x28, 0xB5, 0x2F, 0xFD);
use constant MAGIC_XZ   => pack('C6', 0xfd, 0x37, 0x7a, 0x58, 0x5a, 0x00);

sub new {

    my ($class,$fn, %args) = @_;

    my $self = bless {} => $class;

    # 'fast' mode turns off parser sanity-checking in places
    if ($args{fast}) {
        $self->fast( $args{fast} );
    }

    if (defined $fn) {

        my $fh = openhandle($fn); # can pass filehandle too;
        if (! defined $fh) { # otherwise assume filename