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);


my %p = (
    'annotate'             => 0,
    'bam_to_bed'           => 2,
    'bed_to_bam'           => 1,
    'bed_to_IGV'           => 5,
    'b12_to_b6'            => 0,
    'closest'              => 1,
    'complement'           => 0,
    'coverage'             => 0,
    'fasta_from_bed'       => 0,
    'genome_coverage'      => 2,
    'graph_union'          => 2,
    'group_by'             => 3,
    'intersect'            => 1,
    'links'                => 3,
    'mask_fasta_from_bed'  => 0,
    'merge'                => 1,
    'overlap'              => 1,
    'pair_to_bed'          => 2,
    'pair_to_pair'         => 3,
    'shuffle'              => 2,
    'slop'                 => 3,
    'sort'                 => 0,
    'subtract'             => 1,
    'window'               => 3
     );

my %s = (
    'annotate'             => 4,
    'bam_to_bed'           => 6,
    'bed_to_bam'           => 2,
    'bed_to_IGV'           => 2,
    'b12_to_b6'            => 0,
    'closest'              => 2,
    'complement'           => 0,
    'coverage'             => 4,
    'fasta_from_bed'       => 3,
    'genome_coverage'      => 4,
    'graph_union'          => 2,
    'group_by'             => 0,
    'intersect'            => 11,
    'links'                => 0,
    'mask_fasta_from_bed'  => 1,
    'merge'                => 3,
    'overlap'              => 0,
    'pair_to_bed'          => 4,
    'pair_to_pair'         => 3,
    'shuffle'              => 1,
    'slop'                 => 1,
    'sort'                 => 6,
    'subtract'             => 1,
    'window'               => 5
    );

my $bam_file = test_input_file('Ft.bam');
my $bed_file = test_input_file('Ft.bed');
my $bed12_file = test_input_file('Ft.bed12');
my $fas_file = test_input_file('Ft.frag.fas');
my $bedpe1_file = test_input_file('e_coli_1.bedpe');
my $bedpe2_file = test_input_file('e_coli_2.bedpe');
my $bed3_file = test_input_file('e_coli.bed3');
my $bg1_file = test_input_file('1.bg');
my $bg2_file = test_input_file('2.bg');
my $bg3_file = test_input_file('3.bg');

my %format_lookup = (
    'annotate'             => 'bed',
    'bam_to_bed'           => 'bed',
    'bed_to_bam'           => 'bam',
    'bed_to_IGV'           => 'igv',
    'b12_to_b6'            => 'bed',
    'closest'              => 'bedpe',
    'complement'           => 'bed',
    'coverage'             => 'bed',
    'fasta_from_bed'       => 'fasta',
    'genome_coverage'      => 'tab',
    'graph_union'          => 'bg',
    'group_by'             => 'bed',
    'intersect'            => 'bed|bam',
    'links'                => 'html',
    'mask_fasta_from_bed'  => 'fasta',
    'merge'                => 'bed',
    'overlap'              => 'bed',
    'pair_to_bed'          => 'bedpe|bam',
    'pair_to_pair'         => 'bedpe',
    'slop'                 => 'bed',
    'shuffle'              => 'bed',
    'sort'                 => 'bed',
    'subtract'             => 'bed',
    'window'               => 'bedpe'
    );

my %result_lookup = (
    'annotate'             => 1385,  # OK
    'bam_to_bed'           => 1385,  # OK
    'fasta_from_bed'       => 1385,  # OK
    'mask_fasta_from_bed'  => 1,     # OK
    'shuffle'              => 828,   # OK
    'window'               => 74998, # OK
    'closest'              => 845,   # OK
    'genome_coverage'      => 38,    # OK
    'merge'                => 242,   # OK
    'slop'                 => 828,   # OK
    'complement'           => 291,   # OK - change in data provided by BEDTools or behaviour of complementBed? was 243
    'intersect'            => 72534, # OK
    'pair_to_bed'          => 2,     # OK
    'sort'                 => 828,   # OK
    'coverage'             => 57261, # OK
    'links'                => 11603, # OK
    'pair_to_pair'         => 497,   # OK
    'subtract'             => 57959, # OK
    'group_by'             => 1,     # OK
    'b12_to_b6'            => 1385,  # OK
    'overlap'              => 500    # OK
    );

SKIP : {
    test_skip( -requires_executable => $bedtoolsfac,