fix truncation of results in phased queries where checkAminoAcidChang…

…e=TRUE
julie-sullivan · May 10, 2024 · c627596 · c627596
1 parent 596816d
commit c627596
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Showing 2 changed files with 37 additions and 41 deletions.
diff --git a/...ore/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java b/...ore/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java
@@ -34,57 +34,53 @@ public List<CellBaseDataResult<Variant>> run(List<Variant> variantList,
             CellBaseDataResult<Variant> variantCellBaseDataResult = variantCellBaseDataResultList.get(j);
             if (variantCellBaseDataResult != null && variantCellBaseDataResult.getResults() != null
                     && !variantCellBaseDataResult.getResults().isEmpty()) {
-                // Variants are normalised and data from each of the sources (COSMIC, ClinVar, DOCM, etc.) integrated
-                // during the build process. Only one variant record should be present per assembly.
-                if (variantCellBaseDataResult.getResults().size() > 1) {
-                    logger.warn("More than one result found either the clinical_variants or variation collection"
-                            + "for variant " + variantCellBaseDataResult.getId() + ". Arbitrarily selecting the first one. "
-                            + "Please, check.");
-                }
-
-                Variant matchedVariant = variantCellBaseDataResult.getResults().get(0);
                 Variant queryVariant = variantList.get(j);
-                List<T> annotationObjectList = getAnnotationObjectList(matchedVariant);
-                // Phase is stored at the evidence entry/population frequency level, e.g.: there might be two ClinVar
-                // RCVs for one variant:
-                //   - In the first the variant is submitted as part of an MNV and therefore it is phased
-                //   - In the second one the variant is submitted singleton and therefore it is not phased
-                // both RCVs will be integrated in the same Variant object after decomposition as separate EvidenceEntry
-                // objects, each with its corresponding phase information
-                int i = 0;
-                while (i < annotationObjectList.size()) {
-                    T annotationObject = annotationObjectList.get(i);
-                    List<Variant> databaseHaplotype = getHaplotype(annotationObject, matchedVariant);
-                    // Haplotype empty if EvidenceEntry/PopulationFrequency is not phased
-                    if (databaseHaplotype.isEmpty()) {
-                        i++;
-                    } else {
-                        // Sample   Cellbase  Match
-                        // -------------------------------
-                        // SNV      MNV       X
-                        // MNV      MNV       ✓
-                        // Missing genotypes in the input list will be considered as wildcards towards finding a
-                        // matching haplotype (MNV) in the input list, since otherwise the clinical variant would not be
-                        // returned
-                        if (sameHaplotype(queryVariant, variantList, databaseHaplotype)) {
+                boolean queryVariantHasTraitAssociations = false;
+                for (Variant matchedVariant: variantCellBaseDataResult.getResults()) {
+                    List<T> annotationObjectList = getAnnotationObjectList(matchedVariant);
+                    // Phase is stored at the evidence entry/population frequency level, e.g.: there might be two ClinVar
+                    // RCVs for one variant:
+                    //   - In the first the variant is submitted as part of an MNV and therefore it is phased
+                    //   - In the second one the variant is submitted singleton and therefore it is not phased
+                    // both RCVs will be integrated in the same Variant object after decomposition as separate EvidenceEntry
+                    // objects, each with its corresponding phase information
+                    int i = 0;
+                    while (i < annotationObjectList.size()) {
+                        T annotationObject = annotationObjectList.get(i);
+                        List<Variant> databaseHaplotype = getHaplotype(annotationObject, matchedVariant);
+                        // Haplotype empty if EvidenceEntry/PopulationFrequency is not phased
+                        if (databaseHaplotype.isEmpty()) {
                             i++;
                         } else {
-                            annotationObjectList.remove(i);
+                            boolean queryVariantInDBHaplotype = getVariant(databaseHaplotype, queryVariant) != null;
+                            // Sample   Cellbase  Match
+                            // -------------------------------
+                            // SNV      MNV       X
+                            // MNV      MNV       ✓
+                            // Missing genotypes in the input list will be considered as wildcards towards finding a
+                            // matching haplotype (MNV) in the input list, since otherwise the clinical variant would not be
+                            // returned
+                            if (queryVariantInDBHaplotype && sameHaplotype(queryVariant, variantList, databaseHaplotype)) {
+                                i++;
+                            } else {
+                                annotationObjectList.remove(i);
+                            }
+                            // Sample   Cellbase  Match
+                            // -------------------------------
+                            // SNV      SNV       ✓
+                            // MNV      SNV       ✓
                         }
-                        // Sample   Cellbase  Match
-                        // -------------------------------
-                        // SNV      SNV       ✓
-                        // MNV      SNV       ✓
+                    }
+                    if (!annotationObjectList.isEmpty()) {
+                        queryVariantHasTraitAssociations = true;
                     }
                 }
-
                 // Remove whole variant from the query result object if ended up without any evidence entry
-                if (annotationObjectList.isEmpty()) {
+                if (!queryVariantHasTraitAssociations) {
                     reset(variantCellBaseDataResult);
                 }
             }
         }
-
         return variantCellBaseDataResultList;
     }
 

diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java
@@ -87,7 +87,7 @@ public static boolean isMissing(String field) {
         return StringUtils.isBlank(field) || field.equals(MISSING_VALUE);
     }
 
-    private Variant getVariant(List<Variant> variantList, Variant variant) {
+    protected Variant getVariant(List<Variant> variantList, Variant variant) {
         for (Variant variant1 : variantList) {
             // TODO: simple chr, start, ref, alt matching here - shall implement something fancier
             if (variant.getChromosome().equals(variant1.getChromosome())