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BEGIN {use_ok( 'NGS::Tools::BAMSurgeon' )};
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;
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