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Merge 7a55ec8 into cafe03e
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marcoooo committed Feb 18, 2021
2 parents cafe03e + 7a55ec8 commit 4a71037
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/BaseCheck.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AlignFeatureExternalDB.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AlignmentCoordinates.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AltAllele.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AltAlleleGroup.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AnalysisDescription.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AnalysisFormat.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/Archive.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/ArraysHaveProbes.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AssemblyExceptions.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AssemblySeqregion.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesCoverage.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesExist.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/BlankEnums.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/BlankNulls.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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8 changes: 4 additions & 4 deletions lib/Bio/EnsEMBL/DataCheck/Checks/BlankSets.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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use constant {
NAME => 'BlankSets',
DESCRIPTION => 'Set columns do not have empty string values (unless default)',
GROUPS => ['variation'],
DB_TYPES => ['variation']
GROUPS => ['core', 'corelike', 'variation'],
DB_TYPES => ['cdna', 'core', 'otherfeatures', 'rnaseq', 'variation']
};

sub tests {
Expand All @@ -43,7 +43,7 @@ sub tests {
WHERE
TABLE_SCHEMA = database() AND
DATA_TYPE = 'set' AND
COLUMN_DEFAULT <> ''
(COLUMN_DEFAULT <> '' OR COLUMN_DEFAULT IS NULL)
/;

my $sets = $self->dba->dbc->sql_helper->execute(-SQL => $set_sql);
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CanonicalTranscripts.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckCAFETable.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckComparaStableIDs.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckConservationScore.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckEmptyLeavesTrees.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckFamiliesMLSS.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckFlatProteinTrees.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckGOCScoreStats.pm
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=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckGeneGainLossData.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckGeneTreeRootMLSS.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckGenomicAlignMTs.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckGenomicAlignments.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckHomology.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckHomologyMLSS.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckJSONObjects.pm
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=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckLastZCoverage.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckMSANames.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion lib/Bio/EnsEMBL/DataCheck/Checks/CheckOntologyTerm.pm
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2020] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
=head1 LICENSE
Copyright [2018-2019] EMBL-European Bioinformatics Institute
Copyright [2018-2021] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the 'License');
you may not use this file except in compliance with the License.
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