Default clin_sig_allele to 1 (#558)

* Default clin_sig_allele to 1

modules/Bio/EnsEMBL/VEP/Config.pm

@@ -100,6 +100,7 @@ our %DEFAULTS = (
   vcf_info_field    => 'CSQ',
   ucsc_data_root    => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
   max_sv_size       => 10000000,
+  clin_sig_allele   => 1,
 
   # frequency filtering
   freq_freq         => 0.01,

t/Runner.t

@@ -219,7 +219,7 @@ is_deeply($runner->get_OutputFactory, bless( {
   'mirna' => undef,
   'ambiguity' => undef,
   'vcf_string' => undef,
-  'clin_sig_allele' => undef,
+  'clin_sig_allele' => 1,
 }, 'Bio::EnsEMBL::VEP::OutputFactory::VEP_output' ), 'get_OutputFactory');
 
 

vep

@@ -101,9 +101,9 @@ GetOptions(
   'dont_skip',               # don't skip vars that fail validation
   'nearest=s',               # get nearest transcript, gene or symbol (for gene)
   'distance=s',              # set up/downstream distance
-  'clin_sig_allele',         # use allele specific clinical significance data where it exists
+  'clin_sig_allele=i',       # use allele specific clinical significance data where it exists
   'overlaps',                # report length and percent of a transcript or regulatory feature overlaped with a SV
-  'max_sv_size=i',             # modify the size of structural variant to be handled (limited by default to reduce memory requirements)
+  'max_sv_size=i',           # modify the size of structural variant to be handled (limited by default to reduce memory requirements)
 
   # verbosity options
   'verbose|v',               # print out a bit more info while running