if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; }
elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; }
elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }
if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; }
elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; }
elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }