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This queue is for tickets about the bioperl CPAN distribution.

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The Basics
Id: 44782
Status: resolved
Priority: 0/
Queue: bioperl

Owner: Nobody in particular
Requestors: allenday [...]

Bug Information
Severity: Normal
Broken in: 1.6.0
Fixed in: (no value)


Subject: Bio::SearchIO::Writer::Gbrowse e-value vs. score
Small typo preventing the e-value from being used in the GFF score field. See attached patch.
--- ./ 2009-04-03 09:53:23.000000000 -0400 +++ ./ 2009-04-03 09:51:42.000000000 -0400 @@ -94,7 +94,7 @@ sub new { ($self->{'_evalue'}, $self->{'_cigar'}, $self->{'_prefix'}, - $self->{'signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX + $self->{'_signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX OUTPUT_SIGNIF)], @args); $self->{'_evalue'} && warn( "Use of the -e_value argument is deprecated.\nIn future, use \$writer->filter(\"type\", \&code) instead.\n\tparsing will proceed correctly with this e_value\n"); $self->{Gbrowse_HSPID} = 0;
Patch committed to bioperl svn. Thanks Allen!

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