Merge pull request #246 from ens-lgil/release/93

Filter on VCF even if there is no VEP annotation and minor fix on VEP installation
Ensembl · Jul 24, 2018 · e2669dc · e2669dc
2 parents 6895f64 + 6ed7e8f
commit e2669dc
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/INSTALL.pl b/INSTALL.pl
@@ -1694,7 +1694,7 @@ sub download_to_file {
 
   if($CAN_USE_CURL) {
     my $response = `curl -s -o $file -w '%{http_code}' --location "$url" `;
-    if ( $response != 200) {
+    if ( $response != 200 && $response != 226) {
       print "curl failed ($response), trying to fetch using LWP::Simple\n" unless $QUIET;
       $CAN_USE_CURL = 0;
       download_to_file($url, $file);

diff --git a/filter_vep b/filter_vep
@@ -245,6 +245,8 @@ sub main {
             map {parse_line($_, \@headers, '\|', $main_data)}
             @chunks;
         }
+        # Rare case where no CSQ stuff found
+        push @data, $main_data if (!@data);
 
         $filter_set->limit_synonym_search(1);
       }

diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 93;
-our $VEP_SUB_VERSION = 0;
+our $VEP_SUB_VERSION = 1;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS