ENSCORESW-1120: added is_high_coverage flag for genome container

modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm

@@ -1189,6 +1189,39 @@ sub has_karyotype {
   return 1;
 }
 
+
+=head2 is_high_coverage
+
+  Arg        : None
+  Example    : $is_high_coverage = $genome->is_high_coverage();
+  Description: Boolean indicating whether an assembly is high coverage
+               or not
+  Returntype : integer
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub is_high_coverage {
+  my $self = shift;
+
+  my $coverage_depth = $self->_meta_container->single_value_by_key('assembly.coverage_depth');
+
+  return 0 if !$coverage_depth;
+  $coverage_depth = lc($coverage_depth);
+
+  if ($coverage_depth eq 'high') {
+    return 1;
+  } elsif (($coverage_depth eq 'low') or ($coverage_depth eq 'medium')) {
+    return 0;
+  } elsif ($coverage_depth =~ /^([0-9]+)x$/) {
+    return $1<6 ? 0 : 1;
+  }
+
+  return 0;
+}
+
 =head2 is_polyploid
 
   Arg        : None

modules/t/genomeContainer.t

@@ -15,6 +15,7 @@
 use strict;
 use warnings;
 
+use Test::Warnings;
 use Bio::EnsEMBL::DBSQL::GenomeContainer;
 use Bio::EnsEMBL::Test::TestUtils;
 use Bio::EnsEMBL::Registry;
@@ -154,15 +155,24 @@ my $alt_transcript_count = $sql_helper->execute_single_result(-SQL => $alt_trans
 is($alt_transcript_count, $genome->get_alt_transcript_count(), "Number of alt transcripts is correct");
 
 
-# 
+#
 # Test karyotype flag
 #
 
-is(1, $genome->has_karyotype, "Human has some chromosomes");
 my $empty_db = $multi->get_DBAdaptor("empty");
 my $empty_genome = $empty_db->get_adaptor('GenomeContainer');
+
+is(1, $genome->has_karyotype, "Human has some chromosomes");
 is(0, $empty_genome->has_karyotype, "Empty db does not have chromosomes");
 
+
+#
+# Test high coverage flag
+#
+
+is(1, $genome->is_high_coverage, "Human genebuild is high coverage");
+is(0, $empty_genome->is_high_coverage, "Empty db is not high coverage");
+
 #
 # Test polyploid genome support
 #