File Coverage

blib/lib/BioX/Seq/Stream.pm

Criterion	Covered	Total	%
statement	106	106	100.0
branch	46	52	90.3
condition	1	2	50.0
subroutine	20	20	100.0
pod	2	2	100.0
total	175	182	96.7

package BioX::Seq::Stream;

use 5.012;
use strict;
use warnings;

use IPC::Cmd qw/can_run/;
use Scalar::Util qw/blessed openhandle/;
use BioX::Seq;
use POSIX qw/ceil/;
use Cwd qw/abs_path/;
use File::Basename qw/fileparse/;

# define or search for binary locations
# if these are not available
our $GZIP_BIN = can_run('pigz')   // can_run('gzip');
our $BZIP_BIN = can_run('pbzip2') // can_run('bzip2');
our $ZSTD_BIN = can_run('pzstd')  // can_run('zstd');
our $DSRC_BIN = can_run('dsrc2')  // can_run('dsrc');
our $FQZC_BIN = can_run('fqz_comp');
our $XZ_BIN   = can_run('xz');

use constant MAGIC_GZIP => pack('C3', 0x1f, 0x8b, 0x08);
use constant MAGIC_DSRC => pack('C2', 0xaa, 0x02);
use constant MAGIC_BZIP => 'BZh';
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

            #if passed a filename, try to determine if compressed
            open $fh, '<', $fn or die "Error opening $fn for reading\n";

            #read first six bytes as raw
            #this causes a memory leak as opened filehandles are not properly
            #closed again. Should work without setting binary mode anyway.
            #my $old_layers = join '', map {":$_"} PerlIO::get_layers($fh);
            #binmode($fh);
            read( $fh, my $magic, 6 );
            #binmode($fh, $old_layers);

            #check for compression and open stream if found
            if (substr($magic,0,3) eq MAGIC_GZIP) {
                close $fh;
                if (! defined $GZIP_BIN) {
                    # fall back on Perl-based method (but can be SLOOOOOW!)
                    require IO::Uncompress::Gunzip;
                    $fh = IO::Uncompress::Gunzip->new($fn, MultiStream => 1);
                }
                else {
                    open $fh, '-|', $GZIP_BIN, '-dc', $fn
                        or die "Error opening gzip stream: $!\n";
                }
            }
            elsif (substr($magic,0,3) eq MAGIC_BZIP) {
                close $fh;
                if (! defined $BZIP_BIN) {
                    # fall back on Perl-based method (but can be SLOOOOOW!)
                    require IO::Uncompress::Bunzip2;
                    $fh = IO::Uncompress::Bunzip2->new($fn, MultiStream => 1);
                }
                else {
                    open $fh, '-|', $BZIP_BIN, '-dc', $fn
                        or die "Error opening bzip2 stream: $!\n";
                }
            }
            elsif (substr($magic,0,4) eq MAGIC_ZSTD) {
                die "no zstd backend found\n" if (! defined $ZSTD_BIN);
                close $fh;
                open $fh, '-|', $ZSTD_BIN, '-dc', $fn
                    or die "Error opening zstd stream: $!\n";
            }
            elsif (substr($magic,0,2) eq MAGIC_DSRC) {
                die "no dsrc backend found\n" if (! defined $DSRC_BIN);
                close $fh;
                open $fh, '-|', $DSRC_BIN, 'd', '-s', $fn
                    or die "Error opening dsrc stream: $!\n";
            }
            elsif (substr($magic,0,4) eq MAGIC_FQZC) {
                die "no fqz backend found\n" if (! defined $FQZC_BIN);
                close $fh;
                open $fh, '-|', $FQZC_BIN, '-d', $fn
                    or die "Error opening fqz_comp stream: $!\n";
            }
            elsif (substr($magic,0,6) eq MAGIC_XZ) {
                die "no xz backend found\n" if (! defined $XZ_BIN);
                close $fh;
                open $fh, '-|', $XZ_BIN, '-dc', $fn
                    or die "Error opening xz stream: $!\n";
            }
            else {
                seek($fh,0,0);
            }

        }
        $self->{fh} = $fh;

    }
    else {
        $self->{fh} = \*STDIN;
    }

    # handle files coming from different platforms
    #my @layers = PerlIO::get_layers($self->{fh});
    #binmode($self->{fh},':unix:stdio:crlf');

    $self->_guess_format;

    $self->_init;

    return $self;

}

sub fast {

    my ($self, $bool) = @_;
    $self->{fast} = $bool // 1;

}

sub _guess_format {

    my ($self) = @_;

    # Filetype guessing must be based on first two bytes (or less)
    # which are stored in an object buffer
    my $r = (read $self->{fh}, $self->{buffer}, 2);
    die "failed to read initial bytes" if ($r != 2);

    my $search_path = abs_path(__FILE__);
    $search_path =~ s/\.pm$//i;
    my @matched;
    for my $module ( glob "$search_path/*.pm" ) {
        my ($name,$path,$suff) = fileparse($module, qr/\.pm/i);
        my $classname = blessed($self) . "::$name";
        eval "require $classname";
        if ($classname->_check_type($self)) {
            push @matched, $classname;
        }
    }

    die "Failed to guess filetype\n"   if (scalar(@matched) < 1);
    # uncoverable branch true
    die "Multiple filetypes matched\n" if (scalar(@matched) > 1);

    eval "require $matched[0]";
    bless $self => $matched[0];

}


1;


__END__