### 00-test.t #############################################################################
# This file is a template for testing
### Includes ######################################################################################
# Safe Perl
use strict;
use Carp;
use FindBin qw($Bin);
### Tests #################################################################################
# Verify that the module can be included. (BEGIN just makes this happen early)
BEGIN {use_ok('NGS::Tools::BAMSurgeon')};
# Verify some
ok(my $bamsurgeon = NGS::Tools::BAMSurgeon->new(
working_dir => '.',
config => "$Bin/../share/config.yaml",
somatic_profile => "$Bin/../share/somatic.yaml",
germline_profile => "$Bin/../share/germ_mut.yaml",
bam => 'test.bam',
tumour_name => "test",
sex => 'M',
gpercent => 0.7,
seed => 12345,
minvaf => 1,
maxvaf => 1,
vafbeta1 => 2.0,
vafbeta2 => 2.0,
indel_minlen => 1,
indel_maxlen => 90,
indel_types => 'INS,DEL',
sv_minlen => 3000,
sv_maxlen => 30000,
sv_types => 'DUP,INV',
phasing => 0,
redochrs => 'all'
), "Make sure we can instantiate");
done_testing();
1;