ABI

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ABI.pm  view on Meta::CPAN

	$self->{_seq_length}           = 0;
	$self->{_seq_length_corrected} = 0;
	$self->{_abs_index}            = 26;
	$self->{_index}                = undef;
	$self->{PLOC1}                 = undef;
	$self->{PLOC}                  = undef;
	$self->{_a_start}              = undef;
	$self->{_g_start}              = undef;
	$self->{_c_start}              = undef;
	$self->{_t_start}              = undef;
	$self->{DATA9}                 = undef;
	$self->{DATA10}                = undef;
	$self->{DATA11}                = undef;
	$self->{DATA12}                = undef;
	$self->{PBAS1}                 = undef;
	$self->{PBAS2}                 = undef;
	$self->{FWO}                   = undef;
	$self->{_mac_header}           = 0;
	$self->{_maximum_trace}        = 0;

	if ( $self->_is_abi() ) {

		#print "ABI FILE\n";
		$self->_set_index();

ABI.pm  view on Meta::CPAN

	#print $self->{_index};
	seek( $self->{_fh}, $self->{_abs_index} - 8 + $self->{_mac_header}, 0 );
	read( $self->{_fh}, $buf, 4 );
	$num_records = unpack( "N", $buf );
	for ( my $i = 0 ; $i <= $num_records - 1 ; $i++ ) {
		seek( $self->{_fh}, $self->{_index} + ( $i * 28 ), 0 );
		read( $self->{_fh}, $buf, 4 );
		if ( $buf eq "FWO_" ) {
			$self->{FWO} = $self->{_index} + ( $i * 28 ) + 20;
		}
		if ( $buf eq "DATA" ) {
			$data_counter++;
			if ( $data_counter == 9 ) {
				$self->{DATA9} = $self->{_index} + ( $i * 28 ) + 20;
			}
			if ( $data_counter == 10 ) {
				$self->{DATA10} = $self->{_index} + ( $i * 28 ) + 20;
			}
			if ( $data_counter == 11 ) {
				$self->{DATA11} = $self->{_index} + ( $i * 28 ) + 20;
			}
			if ( $data_counter == 12 ) {
				$self->{DATA12} = $self->{_index} + ( $i * 28 ) + 20;
			}
		}
		if ( $buf eq "PBAS" ) {
			$pbas_counter++;
			if ( $pbas_counter == 1 ) {
				$self->{PBAS1} = $self->{_index} + ( $i * 28 ) + 20;
			}
			if ( $pbas_counter == 2 ) {
				$self->{PBAS2} = $self->{_index} + ( $i * 28 ) + 20;
			}

ABI.pm  view on Meta::CPAN

				$self->{PLOC1} = $self->{_index} + ( $i * 28 ) + 20;
			}
			if ( $ploc_counter == 2 ) {
				$self->{PLOC} = $self->{_index} + ( $i * 28 ) + 20;
			}
		}
		if ( $buf eq "SMPL" ) {
			$self->{SMPL} = $self->{_index} + ( $i * 28 ) + 20;
		}
	}
	seek( $self->{_fh}, $self->{DATA12} - 8, 0 );
	read( $self->{_fh}, $buf, 4 );
	$self->{_trace_length} = unpack( "N", $buf );
	seek( $self->{_fh}, $self->{PBAS2} - 4, 0 );
	read( $self->{_fh}, $buf, 4 );
	$self->{_seq_length} = unpack( "N", $buf );
	seek( $self->{_fh}, $self->{PBAS1} - 4, 0 );
	read( $self->{_fh}, $buf, 4 );
	$self->{_seq_length_corrected} = unpack( "N", $buf );
	$self->{PLOC}   = $self->_get_int( $self->{PLOC} ) + $self->{_mac_header};
	$self->{PLOC1}  = $self->_get_int( $self->{PLOC1} ) + $self->{_mac_header};
	$self->{DATA9}  = $self->_get_int( $self->{DATA9} ) + $self->{_mac_header};
	$self->{DATA10} = $self->_get_int( $self->{DATA10} ) + $self->{_mac_header};
	$self->{DATA11} = $self->_get_int( $self->{DATA11} ) + $self->{_mac_header};
	$self->{DATA12} = $self->_get_int( $self->{DATA12} ) + $self->{_mac_header};
	$self->{PBAS1}  = $self->_get_int( $self->{PBAS1} ) + $self->{_mac_header};
	$self->{PBAS2}  = $self->_get_int( $self->{PBAS2} ) + $self->{_mac_header};
	$self->{SMPL} += $self->{_mac_header};
}

sub _set_base_calls {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length} * 2;
	my $fh     = $self->{_fh};

ABI.pm  view on Meta::CPAN

	seek( $fh, $self->{PBAS1}, 0 );
	read( $fh, $buf, $length );
	$self->{_sequence_corrected} = $buf;
}

sub _set_traces {
	my $self = shift;
	my $buf;
	my ( @pointers, @A, @G, @C, @T );
	my (@datas) =
	  ( $self->{DATA9}, $self->{DATA10}, $self->{DATA11}, $self->{DATA12} );
	my $fh = $self->{_fh};
	seek( $fh, $self->{FWO}, 0 );
	read( $fh, $buf, 4 );
	my @order = split( //, $buf );

	#print "@order", "\n";
	for ( my $i = 0 ; $i < 4 ; $i++ ) {
		if ( $order[$i] =~ /A/i ) {
			$pointers[0] = $datas[$i];
		} elsif ( $order[$i] =~ /C/i ) {