my $self      = shift; # Package reference

    # Resetting assembly data structure
    my $Assembly = Bio::Assembly::Scaffold->new(-source=>'phrap');

    # Looping over all phrap out file lines
    my ($contigOBJ);
    while ($_ = $self->_readline) {
	chomp;

	# Loading exact dupicated reads list
#	/Exact duplicate reads:/ && do {
#	    my @exact_dupl;
#	    while (<FILE>) {
#		last if (/^\s*$/);
#		/(\S+)\s+(\S+)/ && do {
#		    push(@exact_dupl,[$1,$2]);
#		};
#		$self->{'assembly'}{'exact_dupl_reads'} =
#		    new Data::Table(\@exact_dupl,['included','excluded'],0);
#	    }
#	};

	# Loading singlets reads data
	/^(\d+) isolated singletons/ && do {
	    while ($_ = $self->_readline) {
		chomp;
		last if (/^$/);
		if (/^\s+(\S+)\s+(\d+)\s+\((\d+)\)/) {
		    my $seqID = $1; my $length = $2;
		    my $nof_trimmed_nonX = $3;
		    my $seq = new Bio::Seq(-strand=>1,
					   -primary_id=>$seqID);
		    my $f = Bio::SeqFeature::Generic->new
			(-start=>1, -end=>$seq->length(),
			 -primary=>$seq->primary_id(),
			 -tag=>{ '_nof_trimmed_nonX' => $nof_trimmed_nonX }
			 );
		    $seq->add_SeqFeature($f);
		    $Assembly->add_singlet($seq);
		}
	    }
	};

	# Loading contig information
	/^Contig (\d+)\.\s+(\d+) reads?; (\d+) bp \(untrimmed\), (\d+) \(trimmed\)\./ && do {
	    my $nof_reads = $2; my $length = $3; my $trimmed_length = $4;
	    $contigOBJ = Bio::Assembly::Contig->new(-id=>$1, -source=>'phrap');
	    my $feat   = Bio::SeqFeature::Generic->new(-start=>1,
						       -end=>$length,
						       -primary=>"_main_contig_feature:".$contigOBJ->id(),
						       -tag=>{ '_trimmed_length' => $trimmed_length }
						       );
	    $contigOBJ->add_features([ $feat ],1);
	    $Assembly->add_contig($contigOBJ);
	};

	# Loading read information
	/^(C?)\s+(-?\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+\(\s*(\d+)\)\s+(\d+\.\d*)\s+(\d+\.\d*)\s+(\d+\.\d*)/ && do {
	    my $strand = ($1 eq 'C' ? -1 : 1);
	    my $readID = $4; my $start = $2; my $end = $3;
	    my $primary_score = $5; my $secondary_score = $6;
	    my $substitutions = $7; my $deletions = $8; my $insertions = $9;
	    my $seq = Bio::LocatableSeq->new(-start=>$start,
					     -end=>$end,
					     -strand=>$strand,
					     -id=>$readID,
					     -primary_id=>$readID,
					     -alphabet=>'dna');
	    my $unalign_coord = Bio::SeqFeature::Generic->new(-start=>$start,
							      -end=>$end,
							      -primary=>"_unalign_coord:$readID",
							      -tag=>{'_primary_score'=>$primary_score,
								     '_secondary_score'=>$secondary_score,
								     '_substitutions'=>$substitutions,
								     '_insertions'=>,$insertions,
								     '_deletions'=>$deletions }
							      );
	    $unalign_coord->attach_seq($seq);
	    $contigOBJ->add_seq($seq); $contigOBJ->add_features([ $unalign_coord ]);
	};

	# Loading INTERNAL clones description
	/INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/ && do {
	    my $contigID = $1;
	    my $contig = $Assembly->get_contig_by_id($contigID);
	    while ($_ = $self->_readline) {
		my (@data,$rejected,$c1_strand,$c2_strand);

		(@data = /\s+(\*?)\s+(C?)\s+(\S+)\s+(C?)\s+(\S+)\s+(-?\d+)\s+(-?\d+)\s+(-?\d+)/) && do {
		    if ($data[0] eq '*') { $rejected = 1 } else { $rejected = 0 }
		    $c1_strand = ($data[1] eq 'C' ? -1 : 1);
		    $c2_strand = ($data[3] eq 'C' ? -1 : 1);
		    (my $clone_name = $data[2]) =~ s/^(\S+)\.\w.*/$1/;
		    my $clone = Bio::SeqFeature::Generic->new(-start=>$data[6],
							      -end=>$data[7],
							      -strand=>0,
							      -primary=>"_internal_clone:$clone_name",
							      -tag=>{'_1st_strand'=>,$c1_strand,
								     '_2nd_strand'=>,$c2_strand,
								     '_1st_name'=>$data[2],
								     '_2nd_name'=>$data[4],
								     '_length'=>$data[5],
								     '_rejected'=>$rejected
								 }
							      );
		    $contig->add_features([ $clone ]);
		};

		/Covered regions:/ && do {
		    my %coord  = /(\d+)/g; my $i = 0;
		    foreach my $start (sort { $a <=> $b } keys %coord) {
			my $cov = Bio::SeqFeature::Generic->new(-start=>$start,
								-end=>$coord{$start},
								-primary=>'_covered_region:'.++$i
								);
			# 1: attach feature to contig consensus, if any
			$contig->add_features([ $cov ],1);
		    }
		    last; # exit while loop
		}; # /Covered regions:/

	    } # while ($_ = $self->_readline)
	}; # /INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/

    } # while ($_ = $self->_readline)
    return $Assembly;

    my $self = shift;

    $self->throw("Writing phrap.out files is not implemented yet! Sorry...");
}

1;

__END__

    # Building an input stream
    use Bio::Assembly::IO;

    # Assembly loading methods
    $io = new Bio::Assembly::IO(-file=>"SGC0-424.phrap.out",
                                -format=>"phrap");

    $assembly = $io->next_assembly;

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  http://bugzilla.bioperl.org/

    Title   : write_assembly
    Usage   : $ass_io->write_assembly($assembly)
    Function: Write the assembly object in Phrap compatible ACE format
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object