From e35d1765096c174b266abd7538a1dee23bb39527 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Fri, 17 Nov 2023 10:33:07 +0100 Subject: [PATCH 1/2] lib: fix HGMD indexer, #TASK-5212 --- .../cellbase/lib/builders/clinical/variant/HGMDIndexer.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java index 4925d8d44c..d2ce12dee8 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java @@ -167,7 +167,7 @@ private boolean updateRocksDB(Variant variant) throws RocksDBException, IOExcept if (normalisedVariantStringList != null) { for (String normalisedVariantString : normalisedVariantStringList) { - VariantAnnotation variantAnnotation = getVariantAnnotation(variant.toString().getBytes()); + VariantAnnotation variantAnnotation = getVariantAnnotation(normalisedVariantString.getBytes()); // Add haplotype property to all EvidenceEntry objects in variant if there are more than 1 variants in // normalisedVariantStringList, i.e. if this variant is part of an MNV (haplotype) From 8d4c3fbc34e992c0509c6d5b68b51634235c48ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Fri, 17 Nov 2023 10:42:42 +0100 Subject: [PATCH 2/2] lib: set data the release in queries where it was missing in the variant annotation calculator, #TASK-5212 --- .../lib/variant/annotation/VariantAnnotationCalculator.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java index d54ceb6623..a16239e879 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java @@ -431,6 +431,7 @@ private List getTargets(Gene mirna) throws QueryException, Ille } } GeneQuery geneQuery = new GeneQuery(); + geneQuery.setDataRelease(dataRelease); geneQuery.setAnnotationTargets(new LogicalList<>(mirnas, false)); List geneMirnaTargets = new ArrayList<>(); List genes = (geneManager.search(geneQuery)).getResults(); @@ -679,9 +680,9 @@ public List getBatchGeneList(List variantList) List geneList = new ArrayList<>(); GeneQuery geneQuery = new GeneQuery(); + geneQuery.setDataRelease(dataRelease); geneQuery.setIncludes(includeGeneFields); geneQuery.setRegions(regionList); - geneQuery.setDataRelease(dataRelease); if (StringUtils.isNotEmpty(consequenceTypeSource)) { // sources can be "ensembl" and/or "refseq". query is validated before execution, will fail if invalid value @@ -1354,6 +1355,7 @@ private boolean[] getRegulatoryRegionOverlaps(String chromosome, Integer start, boolean[] overlapsRegulatoryRegion = {false, false}; RegulationQuery query = new RegulationQuery(); + query.setDataRelease(dataRelease); query.setExcludes(Collections.singletonList("_id")); query.setIncludes(Collections.singletonList("chromosome")); query.setLimit(1);