ABI

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ABI.pm  view on Meta::CPAN

	}
}

sub _set_mac_header {
	my $self = shift;
	$self->{_mac_header} = 128;
}

sub _set_index {
	my $self         = shift;
	my $data_counter = 0;
	my $pbas_counter = 0;
	my $ploc_counter = 0;
	my ( $num_records, $buf );

	#print $self->{_fh}, "\n";
	#print $self->{_mac_header}, "\n";
	seek( $self->{_fh}, $self->{_abs_index} + $self->{_mac_header}, 0 );
	read( $self->{_fh}, $buf, 4 );
	$self->{_index} = unpack( "N", $buf );

ABI.pm  view on Meta::CPAN

	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

	my $fh     = $self->{_fh};
	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 ) {
			$pointers[1] = $datas[$i];
		} elsif ( $order[$i] =~ /G/i ) {
			$pointers[2] = $datas[$i];
		} elsif ( $order[$i] =~ /T/i ) {
			$pointers[3] = $datas[$i];
		} else {
			croak "Wrong traces\n";
		}
	}
	for ( my $i = 0 ; $i < 4 ; $i++ ) {
		seek( $fh, $pointers[$i], 0 );
		read( $fh, $buf, $self->{_trace_length} * 2 );
		if ( $i == 0 ) {
			@A = unpack( "n" x $self->{_trace_length}, $buf );
		}

Changes  view on Meta::CPAN

#$Id: Changes,v 1.1.1.1.2.2 2006/11/20 03:18:12 malay Exp $

Revision history for Perl extension ABI.

1.0  Sat Nov  18  04:22:53 2006
	- Changed to Module::Build system
	- Added test data
	- Changed to Test::More
	- Access to user modified sequence
	- Access to user modified basecalls
	

0.01  Thu May  2 04:22:53 2002
	- original version; created by h2xs 1.21 with options
		-XA -n ABI