fix isolated upstream bug

aparton · Sep 4, 2017 · a813178 · a813178
1 parent 4dd84f6
commit a813178
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Showing 2 changed files with 22 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm
@@ -187,7 +187,7 @@ sub get_all_regions_by_InputBuffer {
     $max = $vf_e if $vf_e > $max;
 
     # convert to region-size
-    my ($r_s, $r_e) = map {int(($_ - 1) / $cache_region_size)} ($vf_s, $vf_e);
+    my ($r_s, $r_e) = map {int(($_ - 1) / $cache_region_size)} ($vf_s - $up_down_size, $vf_e + $up_down_size);
 
     # add all regions between r_s and r_e inclusive
     for(my $s = $r_s; $s <= $r_e; $s++) {

diff --git a/t/AnnotationSource_Database_Transcript.t b/t/AnnotationSource_Database_Transcript.t
@@ -402,6 +402,27 @@ SKIP: {
   $ib->next();
   is_deeply($as->get_all_features_by_InputBuffer($ib), [], 'get_all_features_by_InputBuffer on empty buffer');
 
+  # test upstream
+  $p = Bio::EnsEMBL::VEP::Parser::VCF->new({config => $cfg, file => $test_cfg->create_input_file([qw(21 13002936 . C A)])});
+  $ib = Bio::EnsEMBL::VEP::InputBuffer->new({config => $cfg, parser => $p});
+  $ib->next();
+
+  is_deeply(
+    $as->get_all_regions_by_InputBuffer($ib),
+    [
+      [
+        '21',
+        259
+      ],
+      [
+        '21',
+        260
+      ],
+    ],
+    'get_all_regions_by_InputBuffer - include upstream'
+  );
+
+
   # reset
   $p = Bio::EnsEMBL::VEP::Parser::VCF->new({config => $cfg, file => $test_cfg->{test_vcf}});
   $ib = Bio::EnsEMBL::VEP::InputBuffer->new({config => $cfg, parser => $p});