Merge pull request #792 from jamie-m-a/hotfix/adding_patch_to_testDBs

Adding patch details to test
Ensembl · Feb 18, 2022 · 436d771 · 436d771
2 parents cd70be7 + f7c99a9
commit 436d771
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diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
@@ -127,3 +127,4 @@
 134	\N	patch	patch_105_106_a.sql|schema version
 135	\N	patch	patch_106_107_a.sql|schema version
 136	\N	patch	patch_106_107_b.sql|consequences update
+137	\N	patch	patch_106_107_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -547,7 +547,7 @@ CREATE TABLE `transcript_variation` (
   `feature_stable_id` varchar(128) DEFAULT NULL,
   `allele_string` text,
   `somatic` tinyint(1) NOT NULL DEFAULT '0',
-  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') DEFAULT NULL,
+  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') DEFAULT NULL,
   `cds_start` int(11) unsigned DEFAULT NULL,
   `cds_end` int(11) unsigned DEFAULT NULL,
   `cdna_start` int(11) unsigned DEFAULT NULL,