use
lib dirname(__FILE__);
my
$dir
= dirname(__FILE__);
my
$config_file_path
=
"$dir/test_config.pl"
;
my
$output_directory
=
"$dir/output/"
;
$tp53_mutation_found
= 0;
my
@trans_files
;
$trans_files
[0] =
"$dir/spt/testing_trans_1.spt"
;
$trans_files
[1] =
"$dir/spt/testing_trans_2.spt"
;
my
@cnv_files
;
$cnv_files
[0] =
"$dir/spc/testing_cnv_1.spc"
;
$cnv_files
[1] =
"$dir/spc/testing_cnv_2.spc"
;
mkdir
(
"$output_directory"
,0770)
unless
(-d
"$output_directory"
);
ok(Shatterproof::load_config_file(
$config_file_path
),
'load_config_file'
);
(
$genome_cnv_data_hash_ref
,
$chromosome_copy_number_count_hash_ref
,
$chromosome_cnv_breakpoints_hash_ref
) = Shatterproof::analyze_cnv_data(
$output_directory
, \
@cnv_files
,
$bin_size
, \
$tp53_mutation_found
);
Shatterproof::check_copy_number_switches(
$output_directory
,
$chromosome_copy_number_count_hash_ref
);
my
$test_file
;
my
$ref_file
;
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/copy_number_switches.log"
);
open
(
$ref_file
,
"$dir/ref/copy_number_switches.log.ref"
);
ok(compare(
$test_file
,
$ref_file
)==0,
'check_copy_number_switches-1'
);
close
(
$test_file
);
close
(
$ref_file
);
remove_tree(
"$dir/output"
);