Bugfix100/vcf minimal rejoin (#802)

* increment subversion * add rejoin_variants_in_InputBuffer * add testes for rejoin on minimal
Ensembl · Jul 14, 2020 · 4be118e · 4be118e
1 parent b69359f
commit 4be118e
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Showing 3 changed files with 17 additions and 1 deletion.
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     = 100;
-our $VEP_SUB_VERSION = 2;
+our $VEP_SUB_VERSION = 3;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm
@@ -274,6 +274,8 @@ sub get_all_lines_by_InputBuffer {
   map {@{$self->reset_shifted_positions($_)}}
     @{$buffer->buffer};
 
+  $self->rejoin_variants_in_InputBuffer($buffer) if $buffer->rejoin_required;
+
   foreach my $vf(@{$buffer->buffer}) {
 
     my $line;

diff --git a/t/OutputFactory_VCF.t b/t/OutputFactory_VCF.t
@@ -576,7 +576,21 @@ ok(
   "SV overlap percent and length available"
 );
 
+## rejoin on minimal
 
+$ib = get_runner({
+  input_file => $test_cfg->create_input_file([qw(21 25741665 . CAGAAGAAAG TAGAAGAAAG,C . . .)]),
+  minimal => 1,
+})->get_InputBuffer;
+$of = Bio::EnsEMBL::VEP::OutputFactory::VCF->new({config => $ib->config});
+
+is(scalar @{$ib->buffer}, 2, 'minimal - expanded count');
+is($ib->buffer->[0]->allele_string, 'C/T', 'minimal - expanded first allele string');
+
+$of->rejoin_variants_in_InputBuffer($ib);
+
+is(scalar @{$ib->buffer}, 1, 'minimal - rejoined count');
+is($ib->buffer->[0]->allele_string, 'CAGAAGAAAG/TAGAAGAAAG/C', 'minimal - rejoined allele string');
 
 
 ## test getting stuff from input