errors in pod

[osallou]

Hi, in v2.42, I found several errors in POD structure, preventing the pod2man transformation, plus a few typo errors. Follows a patch to fix those errors. I am not a pod expert, fixes remove errors but you may check what is best appropriate.

Patch to correct POD-generated manual pages - Olivier Sallou - February 2011 --- a/bin/gtf2gff3.pl +++ b/bin/gtf2gff3.pl @@ -1320,7 +1320,7 @@

=head1 NAME

-gtf2gff3 +gtf2gff3 - Converts GTF formatted files to valid GFF3 files

=head1 VERSION

@@ -1496,7 +1496,7 @@ =item C<< FATAL: Invalid value passed to strand: strand. >>

This may indicate that your GTF file does not indicate the strand for -features that require it. Consider using the DEFAULT_STRAND paramater +features that require it. Consider using the DEFAULT_STRAND parameter in the config file. It may also indicate a software bug. Please contact the author.

--- a/bin/wiggle2gff3.pl +++ b/bin/wiggle2gff3.pl @@ -2,7 +2,7 @@

=head1 NAME

-wiggle2gff3.pl +wiggle2gff3.pl - Converts UCSC WIG format files into gff3 files

=head1 SYNOPSIS

--- a/lib/Bio/DB/GFF/Aggregator/match_gap.pm +++ b/lib/Bio/DB/GFF/Aggregator/match_gap.pm @@ -34,7 +34,6 @@ should be sufficient for simple nucleotide to nucleotide alignments.

-################################################################################

=cut

--- a/lib/Bio/DB/GFF/Aggregator/reftranscript.pm +++ b/lib/Bio/DB/GFF/Aggregator/reftranscript.pm @@ -1,6 +1,6 @@ =head1 NAME

-package Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts +Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts

=head1 SYNOPSIS

--- a/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm +++ b/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm @@ -23,7 +23,6 @@

=head2 METHODS

-=over 4

=cut

--- a/lib/Bio/Graphics/Browser2/DataBase.pm +++ b/lib/Bio/Graphics/Browser2/DataBase.pm @@ -63,12 +63,16 @@ $CACHE->delete($key); }

+=over + =item Bio::Graphics::Browser2::DataBase->clone_databases()

Call this after a fork in the child process to make sure that all open databases have had a chance to clone themselves if they need to. Otherwise you will get random database failures.

+=back + =cut

sub clone_databases { --- a/lib/Bio/Graphics/Browser2/Plugin.pm +++ b/lib/Bio/Graphics/Browser2/Plugin.pm @@ -238,7 +238,7 @@

The purpose of this methods is to suppress the 'Configure...' or 'Find...' title that is printed at the top of the page when the -plugin is loaded. It will return false unless overriden by a plugin where +plugin is loaded. It will return false unless overridden by a plugin where this behaviour is desired.

=item $type = $self->type() --- a/lib/Bio/Graphics/Browser2/Region.pm +++ b/lib/Bio/Graphics/Browser2/Region.pm @@ -3,6 +3,12 @@

provide method for fetching and manipulating the current

region or regions.

+=head1 NAME + +Bio::Graphics::Browser2::Region -- Provide method for fetching and manipulating regions + +=cut + use strict; use warnings; use Bio::Graphics::Browser2::Shellwords; --- a/lib/Bio/Graphics/Browser2/Render.pm +++ b/lib/Bio/Graphics/Browser2/Render.pm @@ -3,6 +3,12 @@ use strict;
use warnings;

+=head1 NAME + +Bio::Graphics::Browser2::Render -- Provide methods to render regions + +=cut + use JSON; use Digest::MD5 'md5_hex'; use CGI qw(:standard param request_method header url iframe img span div br center url_param); --- a/lib/Bio/Graphics/Browser2/RenderPanels.pm +++ b/lib/Bio/Graphics/Browser2/RenderPanels.pm @@ -2,6 +2,13 @@ use strict; use warnings;

+=head1 NAME + +Bio::Graphics::Browser2::RenderPanels-- Provide methods to render a panel + +=cut + + use GD 'gdTransparent','gdStyled';

use Bio::Graphics; --- a/lib/Legacy/Graphics/Browser.pm +++ b/lib/Legacy/Graphics/Browser.pm @@ -4,6 +4,12 @@

This is an old version of Bio::Graphics::Browser retained for gbrowse_syn

It is on the path to deprecation

+=head1 NAME + +Legacy::Graphics::Browser-- Old version, deprecated + +=cut + =head1 METHODS

The remainder of this document describes the methods available to the --- a/lib/Bio/Graphics/Browser2/DataSource.pm +++ b/lib/Bio/Graphics/Browser2/DataSource.pm @@ -31,6 +31,10 @@ } }

+=head1 NAME + +Bio::Graphics::Browser2::DataSource -- DataSource to access data + =head1 SYNOPSIS

=head1 DESCRIPTION @@ -149,6 +153,8 @@ delete $CONFIG_CACHE{$self->config_file}; }

+ +=back =head2 userdata()

$path = $source->userdata(@path_components) @@ -852,6 +858,8 @@ croak "Do not call make_link() on the DataSource. Call it on the Render object"; }

+=over + =item $db = $dsn->databases

Return all named databases from [name:database] tracks. @@ -1086,6 +1094,8 @@ %DB_SETTINGS = (); }

+=back + =head2 generate_image

($url,$path) = generate_image($gd);

[hyphaltip]

A pull request via git would make it easiest to incorporate your changes. If not I expect someone can make these fixes.