[Gmod-gbrowse-cmts] Generic-Genome-Browser/lib/Bio/Graphics/Wiggle Loader.pm, 1.1.2.13, 1.1.2.14

[Lincoln S. <ls...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/Graphics/Wiggle
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv6587/lib/Bio/Graphics/Wiggle

Modified Files:
      Tag: stable
	Loader.pm 
Log Message:
another bug fix in the loading of wig files. The performance optimization was setting the file offsets incorrectly

Index: Loader.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/Graphics/Wiggle/Attic/Loader.pm,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** Loader.pm	21 Feb 2008 18:14:59 -0000	1.1.2.13
--- Loader.pm	22 Feb 2008 14:42:35 -0000	1.1.2.14
***************
*** 323,340 ****
  }
  
- sub updatemm {
-   my $self = shift;
-   my ($chrom,$value) = @_;
-   my $seqids = $self->current_track->{seqids};
-   if (!exists $seqids->{$chrom}{min} ||
-       $value < $seqids->{$chrom}{min}) {
-     $seqids->{$chrom}{min} = $value;
-   }
-   if (!exists $seqids->{$chrom}{max} ||
-       $value > $seqids->{$chrom}{max}) {
-     $seqids->{$chrom}{max} = $value;
-   }
- }
- 
  sub process_bed {
    my $self = shift;
--- 323,326 ----
***************
*** 375,383 ****
    my $start   = $self->{track_options}{start};
    my $step    = $self->{track_options}{step};
    # update span
    $self->{track_options}{span} ||= 1;
!   $self->current_track->{seqids}{$seqid}{start} = $start;
!   $self->current_track->{seqids}{$seqid}{end}   =
!     $self->current_track->{seqids}{$seqid}{start} + $self->{track_options}{span} - 1;
    # write out data in 500K chunks for efficiency
    my @buffer;
--- 361,374 ----
    my $start   = $self->{track_options}{start};
    my $step    = $self->{track_options}{step};
+ 
    # update span
    $self->{track_options}{span} ||= 1;
!   my $chrom = $self->current_track->{seqids}{$seqid};
!   $chrom->{start} = $start 
!       if !defined $chrom->{start} || $chrom->{start} > $start;
!   my $end = $chrom->{start} + $self->{track_options}{span} - 1;
!   $chrom->{end}   = $end
!       if !defined $chrom->{end} || $chrom->{end} < $end;
! 
    # write out data in 500K chunks for efficiency
    my @buffer;
***************
*** 390,400 ****
        $wigfile->set_values($start=>\@buffer);
        @buffer = ();
      }
  
-     # update span
-     $self->current_track->{seqids}{$seqid}{end} = $start+$step-1;
-     $start += $step;
    }
    $wigfile->set_values($start=>\@buffer) if @buffer;
  }
  
--- 381,392 ----
        $wigfile->set_values($start=>\@buffer);
        @buffer = ();
+       my $big_step = $step * @buffer;
+       $start += $big_step;
+       $self->current_track->{seqids}{$seqid}{end} = $start+$big_step-1;
      }
  
    }
    $wigfile->set_values($start=>\@buffer) if @buffer;
+   $self->current_track->{seqids}{$seqid}{end} = $start+@buffer*$step-1;
  }
  
***************
*** 404,407 ****
--- 396,400 ----
    my $seqid   = $self->{track_options}{chrom};
    my $span    = $self->{track_options}{span} || 1;
+   my $chrom   = $self->current_track->{seqids}{$seqid};
    my $wigfile = $self->wigfile($seqid);
    while (<$infh>) {
***************
*** 413,423 ****
  
      # update span
!     $self->current_track->{seqids}{$seqid}{start} = $start
!       unless exists $self->current_track->{seqids}{$seqid}{start}
! 	and $self->current_track->{seqids}{$seqid}{start} < $start;
  
-     $self->current_track->{seqids}{$seqid}{end} = $start + ($span-1)
-       if !defined $self->current_track->{seqids}{$seqid}{end}
- 	|| $self->current_track->{seqids}{$seqid}{end} < $start + ($span-1);
    }
    $self->current_track->{seqids}{$seqid}{end} ||= $self->current_track->{seqids}{$seqid}{start};
--- 406,415 ----
  
      # update span
!     $chrom->{start} = $start 
! 	if !defined $chrom->{start} || $chrom->{start} > $start;
!     my $end = $chrom->{start} + $span - 1;
!     $chrom->{end}   = $end
! 	if !defined $chrom->{end} || $chrom->{end} < $end;
  
    }
    $self->current_track->{seqids}{$seqid}{end} ||= $self->current_track->{seqids}{$seqid}{start};