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Fix EPO-Extended low-coverage species classification #1164

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Merged
TamaraNaboulsi merged 1 commit into from
Jun 1, 2026
+2 −1
Merged

Fix EPO-Extended low-coverage species classification #1164

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3 changes: 2 additions & 1 deletion modules/EnsEMBL/Web/Component/Compara_Alignments.pm
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Expand Up @@ -120,7 +120,8 @@ sub content {
#find out if this species is low_coverage and the alignment is EPO_EXTENDED/EPO_LOW_COVERAGE
if ($method_type =~ /(EPO_EXTENDED|EPO_LOW_COVERAGE)/ && @$align_blocks) {
# The species is not low-coverage if it's been used in one of the EPO alignments
$is_low_coverage_species = !scalar( grep {($_->{type} eq 'EPO') && $_->{species}->{$object->species}}
my $prod_name = $hub->species_defs->get_config($object->species, 'SPECIES_PRODUCTION_NAME');
$is_low_coverage_species = !scalar( grep {($_->{type} eq 'EPO') && $_->{species}->{$prod_name}}
values %{$hub->species_defs->multi_hash->{'DATABASE_COMPARA'}{'ALIGNMENTS'}}
);
} elsif ($target_slice && $method_type eq 'CACTUS_DB') {
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