Allow safe mode to override incompatible option checks

Ensembl · Dec 16, 2016 · 4e8d26e · 4e8d26e
1 parent ce97abd
commit 4e8d26e
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Config.pm b/modules/Bio/EnsEMBL/VEP/Config.pm
@@ -449,9 +449,11 @@ sub check_config {
   }
 
   # check incompatible flags
-  foreach my $flag(grep {$config->{$_}} keys %INCOMPATIBLE) {
-    foreach my $invalid(grep {$config->{$_}} @{$INCOMPATIBLE{$flag}}) {
-      throw sprintf("ERROR: Can't use --%s and --%s together\n", $flag, $invalid);
+  unless($config->{safe}) {
+    foreach my $flag(grep {$config->{$_}} keys %INCOMPATIBLE) {
+      foreach my $invalid(grep {$config->{$_}} @{$INCOMPATIBLE{$flag}}) {
+        throw sprintf("ERROR: Can't use --%s and --%s together\n", $flag, $invalid);
+      }
     }
   }
 

diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -20,7 +20,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 87;
-our $VEP_SUB_VERSION = 9;
+our $VEP_SUB_VERSION = 10;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/t/Config.t b/t/Config.t
@@ -111,6 +111,9 @@ throws_ok { Bio::EnsEMBL::VEP::Config->new({format => 'gobbledegook'}) } qr/not
 # incompatible flags
 throws_ok { Bio::EnsEMBL::VEP::Config->new({database => 1, cache => 1}) } qr/Can\'t use.+together/, 'incompatible params';
 
+# incompatible ok with safe on
+ok(Bio::EnsEMBL::VEP::Config->new({safe => 1, most_severe => 1, symbol => 1}), 'incompatible pass with safe');
+
 # missing database/cache/offline
 throws_ok { Bio::EnsEMBL::VEP::Config->new({database => 0}) } qr/The VEP can read gene data from/, 'no database/cache/offline';