[Bioperl-l] hapmap.pm startingcol now 11?

[rich]

Hi,

yes,  you're right.
Jason, I seem to remember you were going to give me cvs access to make 
fixes. Could you give me access so that I can make the change?

cheers
Rich


Albert Vilella wrote:

>Hi all,
>
>AFAICS, Hapmap dump files have (since Dec 2004?) an extra field previous
>to the starting column for the first genotype, so the $startingcol in
>hapmap.pm should change from 10 to 11 (see end of message).
>
>Can anyone confirm? 
>
>I'm getting a MSG:
>
>-------------------- WARNING ---------------------
>MSG: cannot add NA06993 as a genotype skipping
>--------------------------------------------------
>
>And I'm not sure is related to this or not,
>
>Bests,
>
>    Albert.
>
>hapmap.pm
>---------------------------
>sub _pivot {
>    my ($self) = @_;
>
>    my (@cols, at rows, at idheader);
>    while ($_ = $self->_readline){
>	chomp($_);
>	next if( /^\s*\#/ || /^\s+$/ || ! length($_) );
>	if( /^rs\#\s+alleles\s+chrom\s+pos\s+strand/ ) {
>	    @idheader = split $self->flag('field_delimiter');
>	} else { 
>	    push @cols, [split $self->flag('field_delimiter')];
>	}
>    }
>    #Post Dec 2004. Previously was 10
>    my $startingcol = 11;
>
>    $self->{'_header'} = [ map { $_->[0] } @cols];
>    for my $n ($startingcol.. $#{ $cols[ 0 ]}) { 
>	my $column = [ $idheader[$n],
>		       map{ $_->[ $n ] } @cols ];	
>	push (@rows, $column); 
>    }
>    $self->{'_pivot'} = [@rows];
>    $self->{'_i'} = 0;
>}
>---------------------------
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