GMOD/GBrowse — Issue #10: errors in pod
Author: osallou
Created: 2011-10-19 06:31:40+00:00
State: open

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);