Merge pull request #431 from ens-lgil/bugfix/missing_ref_allele_97

Fix issue when the reference allele is missing in the variant allele …

.travis.yml

@@ -3,6 +3,9 @@ language: perl
 os:
   - linux
 
+dist:
+  - trusty
+
 perl:
   - '5.14'
   - '5.26'

modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm

@@ -749,7 +749,6 @@ sub get_hgvs_alleles{
       $ref_allele = $string;
     }
   }
-
   # no change
   elsif ($description =~ m/\=/i) {
     ($ref_allele) = $description =~ m/([A-Z]*)\=$/i;
@@ -1055,26 +1054,28 @@ sub get_matched_variant_alleles {
 
   # convert allele_string key
   foreach my $var($a, $b) {
-    if(my $as = $var->{allele_string}) {
-      my @alleles = split('/', $as);
+    if($var->{allele_string} && $var->{allele_string} !~ /^\/.+$/) {
+      my @alleles = split('/', $var->{allele_string});
       $var->{ref}  ||= shift @alleles;
       $var->{alts}   = \@alleles unless exists($var->{alts});
     }
   }
 
   # check ref
-  throw("Missing ref key in first variant") unless exists($a->{ref});
-  throw("Missing ref key in second variant") unless exists($b->{ref});
+  warning("Missing ref key in first variant") unless exists($a->{ref});
+  warning("Missing ref key in second variant") unless exists($b->{ref});
 
   # check alts
   $a->{alts} ||= [$a->{alt}] if defined($a->{alt});
   $b->{alts} ||= [$b->{alt}] if defined($b->{alt});
-  throw("Missing alt or alts key in first variant") unless exists($a->{alts});
-  throw("Missing alt or alts key in second variant") unless exists($b->{alts});
+  warning("Missing alt or alts key in first variant") unless exists($a->{alts});
+  warning("Missing alt or alts key in second variant") unless exists($b->{alts});
 
   # check pos
-  throw("Missing pos key in first variant") unless $a->{pos};
-  throw("Missing pos key in second variant") unless $b->{pos};
+  warning("Missing pos key in first variant") unless $a->{pos};
+  warning("Missing pos key in second variant") unless $b->{pos};
+
+  return [] if (!exists($a->{ref}) || !exists($b->{ref}) || !exists($a->{alts}) || !exists($b->{alts}) || !$a->{pos} || !$b->{pos});
 
   # munge in strand
   $a->{strand} = 1 unless exists($a->{strand});

modules/t/sequence_utils.t

@@ -18,6 +18,7 @@ use warnings;
 
 use Test::More;
 use Test::Exception;
+use Test::Warnings qw(warning :no_end_test);
 use Bio::EnsEMBL::Test::MultiTestDB;
 
 BEGIN {
@@ -124,14 +125,26 @@ throws_ok {get_matched_variant_alleles({})} qr/undef/, 'get_matched_variant_alle
 throws_ok {get_matched_variant_alleles([])} qr/expected.+HASH/, 'get_matched_variant_alleles - wrong ref type a';
 throws_ok {get_matched_variant_alleles({}, [])} qr/expected.+HASH/, 'get_matched_variant_alleles - wrong ref type b';
 
-throws_ok {get_matched_variant_alleles({}, {})} qr/Missing ref key.+first/, 'get_matched_variant_alleles - missing ref field a';
-throws_ok {get_matched_variant_alleles({ref => 'A'}, {})} qr/Missing ref key.+second/, 'get_matched_variant_alleles - missing ref field b';
+like(
+  (warning { get_matched_variant_alleles({}, {}) })->[0], qr/Missing ref key.+first/, 'get_matched_variant_alleles - missing ref field a'
+);
+like(
+  (warning { get_matched_variant_alleles({ref => 'A'}, {}) })->[0], qr/Missing ref key.+second/, 'get_matched_variant_alleles - missing ref field b'
+);
 
-throws_ok {get_matched_variant_alleles({ref => 'A'}, {ref => 'A'})} qr/Missing alt.+first/, 'get_matched_variant_alleles - missing alts field a';
-throws_ok {get_matched_variant_alleles({ref => 'A', alts => ['B']}, {ref => 'A'})} qr/Missing alt.+second/, 'get_matched_variant_alleles - missing alts field b';
+like(
+  (warning { get_matched_variant_alleles({ref => 'A'}, {ref => 'A'}) })->[0], qr/Missing alt.+first/, 'get_matched_variant_alleles - missing alts field a'
+);
+like(
+  (warning { get_matched_variant_alleles({ref => 'A', alts => ['B']}, {ref => 'A'}) })->[0], qr/Missing alt.+second/, 'get_matched_variant_alleles - missing alts field b'
+);
 
-throws_ok {get_matched_variant_alleles({ref => 'A', alts => ['B']}, {ref => 'A', alts => ['B']})} qr/Missing pos key.+first/, 'get_matched_variant_alleles - missing pos field a';
-throws_ok {get_matched_variant_alleles({ref => 'A', alts => ['B'], pos => 1}, {ref => 'A', alts => ['B']})} qr/Missing pos key.+second/, 'get_matched_variant_alleles - missing pos field b';
+like(
+  warning { get_matched_variant_alleles({ref => 'A', alts => ['B']}, {ref => 'A', alts => ['B'], pos => 2}) }, qr/Missing pos key.+first/, 'get_matched_variant_alleles - missing pos field a'
+);
+like(
+  warning { get_matched_variant_alleles({ref => 'A', alts => ['B'], pos => 1}, {ref => 'A', alts => ['B']}) }, qr/Missing pos key.+second/, 'get_matched_variant_alleles - missing pos field b'
+);
 
 # define tests
 # {