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lib/Bio/AGP/LowLevel.pm  view on Meta::CPAN

  } elsif ( $r{type} =~ /^[ADFGOPW]$/ ) {
      my %descmap = qw/A active_finishing D draft F finished G wgs_finishing N known_gap O other P predraft U unknown_gap W wgs_contig/;
      $r{typedesc} = $descmap{$r{type}}
	or parse_error("unregistered type $r{type}");
      $r{is_gap} = 0;

      @r{qw(ident cstart cend orient)} = @fields;
      if($opt{validate_identifiers}) {
	my $comp_type = identifier_namespace($r{ident})
	  or parse_error("cannot guess type of '$r{ident}'");
      } else {
	$r{ident} or parse_error("invalid identifier '$r{ident}'");
      }

      str_in($r{orient},qw/+ - 0 na/)
	or parse_error("orientation must be one of +,-,0,na");

      $r{cstart} >= 1 && $r{cend} > $r{cstart}
	or parse_error("invalid component start and/or end ($r{cstart},$r{cend})");