From d26b4a3f60dafe9b08fb6cdc28de46d6bf324f05 Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Tue, 24 Jan 2012 14:28:42 +0000
Subject: [PATCH] don't set params value to 1 by default
---
modules/Bio/EnsEMBL/Utils/ConversionSupport.pm | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index e43349fd18..f42f2b3819 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -145,9 +145,9 @@ sub parse_common_options {
s/\s+[;].*$//;
# read options into internal parameter datastructure, removing whitespace
- next unless (/(\w\S*)\s*=*\s*(\S*)\s*/);
+ next unless (/(\w\S*)\s*=\s*(\S*)\s*/);
my $name = $1;
- my $val = $2 || 1;
+ my $val = $2;
if ($val =~ /\$SERVERROOT/) {
$val =~ s/\$SERVERROOT/$serverroot/g;
$val = abs_path($val);
@@ -405,8 +405,8 @@ sub list_all_params {
=cut
sub create_commandline_options {
- my ($self, $settings) = @_;
- my %param_hash;
+ my ($self, $settings, $param_hash) = @_;
+ my %param_hash = $param_hash ? %$param_hash : ();
# get all allowed parameters
if ($settings->{'allowed_params'}) {
@@ -882,7 +882,7 @@ sub get_chrlength {
my $sa = $dba->get_SliceAdaptor;
my @chromosomes = map { $_->seq_region_name }
- @{ $sa->fetch_all($type, $version,$include_non_reference) };
+ @{ $sa->fetch_all($type,$version,$include_non_reference) };
my %chr = map { $_ => $sa->fetch_by_region($type, $_, undef, undef, undef, $version)->length } @chromosomes;
my @wanted = $self->param('chromosomes');
@@ -1636,7 +1636,7 @@ sub get_wanted_chromosomes {
Arg[1] : B::E::Slice
Arg[2] : B::E::DBAdaptor (optional, if you don't supply one then the *first* one you generated is returned, which may or may not be what you want!)
- Example : $genes = $support->get_unique_genes($slice,[$dba]);
+ Example : $genes = $support->get_unique_genes($slice,$dba);
Description : Retrieve genes that are only on the slice itself - used for human where assembly patches
are in the assembly_exception table. Needs the PATCHes to have 'non_ref' seq_region_attributes.
Return type : arrayref of genes
@@ -1655,12 +1655,13 @@ sub get_unique_genes {
my $ga = $dba->get_adaptor('Gene');
my $patch = 0;
my $genes = [];
-
if ( ! $slice->is_reference() ) {
+# if ( 0 ) {
$patch = 1;
my $slices = $sa->fetch_by_region_unique( $slice->coord_system_name(),$slice->seq_region_name() );
foreach my $slice ( @{$slices} ) {
- push @$genes, @{$ga->fetch_all_by_Slice($slice)};
+ push @$genes,@{$ga->fetch_all_by_Slice($slice)};
+ # my $start = $slice->start;
}
}
else {
--
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