#!/usr/bin/env perl
use strict;
use warnings;
use Test::Files qw(compare_ok);
use Cwd;
use File::Path qw( remove_tree );

BEGIN { unshift( @INC, './lib' ) }
BEGIN { unshift( @INC, '../lib' ) }
BEGIN {
    use Test::Most;
    use Test::Files;
    use_ok('Bio::Tradis::CombinePlots');
}

my ( $plotfile, $obj );

$plotfile = "t/data/CombinePlots/comb_sample.txt";

ok( $obj = Bio::Tradis::CombinePlots->new( plotfile => $plotfile ),
    'creating object' );

ok( $obj->combine, 'combining plots' );
ok(
    -e 'combined/first.insert_site_plot.gz',
    'checking first combined plot file exists'
);
ok(
    -e 'combined/second.insert_site_plot.gz',
    'checking second combined plot file exists'
);
ok(
	-e 'comb_sample.stats',
	'checking stats file exists'
);

system("gunzip -c combined/first.insert_site_plot.gz > first.test.plot");
compare_ok(
    'first.test.plot',
    't/data/CombinePlots/first.expected.plot',
    'checking first file contents'
);
system("gunzip -c combined/second.insert_site_plot.gz > second.test.plot");
compare_ok(
    'second.test.plot',
    't/data/CombinePlots/second.expected.plot',
    'checking second file contents'
);
compare_ok(
	'comb_sample.stats',
	't/data/CombinePlots/comb_expected.stats',
	'checking stats file contents'
);

#check with gzipped plots
$plotfile = "t/data/CombinePlots/zip_comb_list.txt";

ok( $obj = Bio::Tradis::CombinePlots->new( plotfile => $plotfile ),
    'creating object' );

ok( $obj->combine, 'combining plots' );
ok(
    -e 'combined/zip_combined.insert_site_plot.gz',
    'checking first combined plot file exists'
);
ok(
    -e 'combined/tabix_sorted.insert_site_plot.gz',
    'checking tabix sorted combined plot file exists'
);

ok(
    -e 'combined/tabix_sorted.insert_site_plot.gz.tbi',
    'checking tabix index file exists'
);


system("gunzip -c combined/zip_combined.insert_site_plot.gz > zip_combined.test.plot");
compare_ok(
    'zip_combined.test.plot',
    't/data/CombinePlots/zip_comb_exp.plot',
    'checking zipped file contents'
);
compare_ok(
	'zip_comb_list.stats',
	't/data/CombinePlots/zip_comb_exp.stats',
	'checking stats file contents'
);

# check custom directory name
$plotfile = "t/data/CombinePlots/comb_sample.txt";
ok( $obj = Bio::Tradis::CombinePlots->new( 
        plotfile     => $plotfile,
        combined_dir => 'comb_test' 
    ),
    'creating object' 
);

ok( $obj->combine, 'combining plots' );
ok( -d 'comb_test', 'checking directory exists' );
ok(
    -e 'comb_test/first.insert_site_plot.gz',
    'checking first combined plot file exists'
);
ok(
    -e 'comb_test/second.insert_site_plot.gz',
    'checking second combined plot file exists'
);

cleanup_files();
done_testing();

sub cleanup_files {
    unlink('first.test.plot');
    unlink('second.test.plot');
    unlink('zip_combined.test.plot');
    unlink('comb_sample.stats');
    unlink('zip_comb_list.stats');
    remove_tree('combined');
    remove_tree('comb_test');
}
