Bio-Tradis

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t/Bio/Tradis/RunTradisBWA.t  view on Meta::CPAN

ok( $obj->_map, 'mapping with custom parameters fine' );


# Check die if ref is not found
$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => "not_really_a_ref.fa",
        tag              => $tag,
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,

    ),
    'creating object'
);
throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; 

t/Bio/Tradis/RunTradisSmalt.t  view on Meta::CPAN

$obj->_remove;
ok( $obj->_map, 'mapping with custom parameters fine' );

# Check die if ref is not found
$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => "not_really_a_ref.fa",
        tag              => $tag,
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,
        smalt_k          => 10,
        smalt_s          => 2
    ),
    'creating object with custom smalt parameters'
);

t/Bio/Tradis/RunTradisTaglessBwa.t  view on Meta::CPAN

ok( $obj->_map, 'mapping with custom parameters fine' );

# Check die if ref is not found
$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => "not_really_a_ref.fa",
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,
      
    ),
    'creating object'
);
throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; 

t/Bio/Tradis/RunTradisTaglessSmalt.t  view on Meta::CPAN

ok( $obj->_map, 'mapping with custom parameters fine' );

# Check die if ref is not found
$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => "not_really_a_ref.fa",
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,
        smalt_k          => 10,
        smalt_s          => 2
    ),
    'creating object with custom smalt parameters'
);
throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown';