EVA-3425 make sure reference and alternate is always upper case (#192)

* make sure reference and alternate is always upper case
EBIvariation · Oct 26, 2023 · e027cbc · e027cbc
1 parent f280604
commit e027cbc
Show file tree

Hide file tree

Showing 24 changed files with 238 additions and 24 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/data/Variant.java b/src/main/java/uk/ac/ebi/eva/commons/models/data/Variant.java
@@ -135,6 +135,8 @@ public Variant(String chromosome, int start, int end, String reference, String a
         this.chromosome = chromosome;
         this.start = start;
         this.end = end;
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() :  null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.reference = (reference != null) ? reference : "";
         this.alternate = (alternate != null) ? alternate : "";
 
@@ -229,7 +231,7 @@ public String getReference() {
     }
 
     public void setReference(String reference) {
-        this.reference = reference;
+        this.reference = reference.toUpperCase();
         this.length = Math.max(reference.length(), alternate.length());
     }
 
@@ -238,7 +240,7 @@ public String getAlternate() {
     }
 
     public void setAlternate(String alternate) {
-        this.alternate = alternate;
+        this.alternate = alternate.toUpperCase();
         this.length = Math.max(reference.length(), alternate.length());
     }
 

diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/data/VariantSourceEntry.java b/src/main/java/uk/ac/ebi/eva/commons/models/data/VariantSourceEntry.java
@@ -22,6 +22,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
+import java.util.stream.Collectors;
 
 /**
  * Entry that associates a variant and a file in a variant archive. It contains
@@ -82,7 +83,7 @@ public VariantSourceEntry(String fileId, String studyId) {
     public VariantSourceEntry(String fileId, String studyId, String[] secondaryAlternates, String format) {
         this.fileId = fileId;
         this.studyId = studyId;
-        this.secondaryAlternates = secondaryAlternates;
+        setSecondaryAlternates(secondaryAlternates);
         this.format = format;
 
         this.samplesData = new ArrayList<>();
@@ -111,7 +112,10 @@ public String[] getSecondaryAlternates() {
     }
 
     public void setSecondaryAlternates(String[] secondaryAlternates) {
-        this.secondaryAlternates = secondaryAlternates;
+        this.secondaryAlternates = secondaryAlternates==null ? new String[0] : Arrays.stream(secondaryAlternates)
+                .map(a->a.toUpperCase())
+                .collect(Collectors.toList())
+                .toArray(new String[0]);
     }
 
     public String getFormat() {

diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/data/VariantStats.java b/src/main/java/uk/ac/ebi/eva/commons/models/data/VariantStats.java
@@ -104,8 +104,8 @@ public VariantStats(String chromosome, int position, String referenceAllele, Str
                         Variant.VariantType variantType, float maf, float mgf, String mafAllele, String mgfGenotype,
                         int numMissingAlleles, int numMissingGenotypes, int numMendelErrors, float percentCasesDominant,
                         float percentControlsDominant, float percentCasesRecessive, float percentControlsRecessive) {
-        this.refAllele = referenceAllele;
-        this.altAllele = alternateAlleles;
+        this.refAllele = Objects.nonNull(referenceAllele) ? referenceAllele.toUpperCase(): null;
+        this.altAllele = Objects.nonNull(alternateAlleles) ? alternateAlleles.toUpperCase(): null;
         this.variantType = variantType;
 
         this.maf = maf;
@@ -134,15 +134,15 @@ public String getRefAllele() {
     }
 
     public void setRefAllele(String refAllele) {
-        this.refAllele = refAllele;
+        this.refAllele = Objects.nonNull(refAllele) ? refAllele.toUpperCase() : null;
     }
 
     public String getAltAllele() {
         return altAllele;
     }
 
     public void setAltAllele(String altAllele) {
-        this.altAllele = altAllele;
+        this.altAllele = Objects.nonNull(altAllele) ? altAllele.toUpperCase() : null;
     }
 
     public Variant.VariantType getVariantType() {

diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/Annotation.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/Annotation.java
@@ -25,6 +25,7 @@
 
 import java.util.Collections;
 import java.util.HashSet;
+import java.util.Objects;
 import java.util.Set;
 
 /**
@@ -83,6 +84,8 @@ public Annotation(String chromosome, int start, int end, String referenceAllele,
         this.vepVersion = vepVersion;
         this.vepCacheVersion = vepCacheVersion;
 
+        referenceAllele = Objects.nonNull(referenceAllele) ? referenceAllele.toUpperCase() : null;
+        alternativeAllele = Objects.nonNull(alternativeAllele) ? alternativeAllele.toUpperCase() : null;
         this.id = buildAnnotationId(chromosome, start, referenceAllele, alternativeAllele, vepVersion, vepCacheVersion);
         this.xrefs = new HashSet<>();
         this.consequenceTypes = new HashSet<>();

diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/VariantDocument.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/VariantDocument.java
@@ -29,6 +29,7 @@
 
 import java.util.HashSet;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 
 /**
@@ -116,6 +117,8 @@ public class VariantDocument {
     public VariantDocument(Variant.VariantType variantType, String chromosome, int start, int end, int length,
                            String reference, String alternate, Map<String, Set<String>> hgvs, Set<String> ids,
                            Set<VariantSourceEntryMongo> variantSources) {
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.id = buildVariantId(chromosome, start, reference, alternate);
         this.variantType = variantType;
         this.chromosome = chromosome;
@@ -139,6 +142,8 @@ public VariantDocument(Variant.VariantType variantType, String chromosome, int s
     public VariantDocument(Variant.VariantType variantType, String chromosome, int start, int end, int length,
                            String reference, String alternate, Set<HgvsMongo> hgvs, Set<String> ids,
                            Set<VariantSourceEntryMongo> variantSources) {
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.id = buildVariantId(chromosome, start, reference, alternate);
         this.variantType = variantType;
         this.chromosome = chromosome;
@@ -160,6 +165,8 @@ public VariantDocument(Variant.VariantType variantType, String chromosome, int s
     }
 
     public static String buildVariantId(String chromosome, int start, String reference, String alternate) {
+        reference = reference.toUpperCase();
+        alternate = alternate.toUpperCase();
         StringBuilder builder = new StringBuilder(chromosome);
         builder.append("_");
         builder.append(start);

diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/projections/SimplifiedVariant.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/projections/SimplifiedVariant.java
@@ -23,6 +23,7 @@
 
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 
 import static uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument.ALTERNATE_FIELD;
@@ -79,6 +80,8 @@ public class SimplifiedVariant {
 
     public SimplifiedVariant(Variant.VariantType variantType, String chromosome, int start, int end, int length,
                              String reference, String alternate, Map<String, Set<String>> hgvs) {
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.id = buildVariantId(chromosome, start, reference, alternate);
         this.variantType = variantType;
         this.chromosome = chromosome;

diff --git a/.../java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java b/.../java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java
@@ -22,11 +22,13 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 /**
  * Mongo database representation of Variant Source entry.
@@ -73,8 +75,10 @@ public VariantSourceEntryMongo(String fileId, String studyId, String[] alternate
         this.fileId = fileId;
         this.studyId = studyId;
         if (alternates != null && alternates.length > 0) {
-            this.alternates = new String[alternates.length];
-            System.arraycopy(alternates, 0, this.alternates, 0, alternates.length);
+            this.alternates = Arrays.stream(alternates)
+                    .map(a->a.toUpperCase())
+                    .collect(Collectors.toList())
+                    .toArray(new String[0]);
         }
         attrs = buildAttributes(attributes);
 

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AccessionReportLineMapper.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AccessionReportLineMapper.java
@@ -21,6 +21,7 @@
 
 import java.util.Arrays;
 import java.util.HashSet;
+import java.util.Objects;
 import java.util.Set;
 
 public class AccessionReportLineMapper extends VariantVcfFactory implements LineMapper<Variant> {
@@ -37,7 +38,7 @@ public Variant mapLine(String line, int lineNumber) {
         String chromosome = fields[0];
         int position = Integer.parseInt(fields[1]);
         String reference = getReference(fields);
-        String alternateAllele = fields[4];
+        String alternateAllele = Objects.nonNull(fields[4]) ? fields[4].toUpperCase() : null ;
 
         VariantCoreFields keyFields = getVariantCoreKeyFields(chromosome, position, reference, alternateAllele);
         Variant variant = new Variant(chromosome, (int) keyFields.getStart(), (int) keyFields.getEnd(), keyFields.getReference(), keyFields.getAlternate());
@@ -48,7 +49,7 @@ public Variant mapLine(String line, int lineNumber) {
     }
 
     private String getReference(String[] fields) {
-        return fields[3].equals(".") ? "" : fields[3];
+        return fields[3].equals(".") ? "" : fields[3].toUpperCase();
     }
 
     private Set<String> getIds(String[] fields) {

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AnnotationLineMapper.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AnnotationLineMapper.java
@@ -182,8 +182,8 @@ private Map<String,String> parseVariant(String variantString, String coordinates
                 parsedVariant.put("chromosome", leftVariantFields[0]);
             }
             parsedVariant.put("start", leftVariantFields[leftVariantFields.length-2]);
-            parsedVariant.put("reference", leftVariantFields[leftVariantFields.length-1]);
-            parsedVariant.put("alternative", variantFields[1]);
+            parsedVariant.put("reference", leftVariantFields[leftVariantFields.length-1].toUpperCase());
+            parsedVariant.put("alternative", variantFields[1].toUpperCase());
         } catch (ArrayIndexOutOfBoundsException e) {
             logger.error("Unexpected variant format for column 1: "+variantString);
             throw e;

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfFactory.java
@@ -37,6 +37,7 @@
 import java.util.TreeMap;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import static java.lang.Math.max;
 
@@ -121,11 +122,14 @@ private Set<String> getIds(String[] fields) {
     }
 
     private String getReference(String[] fields) {
-        return fields[3].equals(".") ? "" : fields[3];
+        return fields[3].equals(".") ? "" : fields[3].toUpperCase();
     }
 
     private String[] getAlternateAlleles(String[] fields, String chromosome, int position, String reference) {
-        return fields[4].split(",");
+        return Arrays.stream(fields[4].split(","))
+                .map(a->a.toUpperCase())
+                .collect(Collectors.toList())
+                .toArray(new String[0]);
     }
 
     private float getQuality(String[] fields) {

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/model/EnsemblVariant.java b/src/main/java/uk/ac/ebi/eva/pipeline/model/EnsemblVariant.java
@@ -52,8 +52,8 @@ public EnsemblVariant(String chromosome, long start, long end, String reference,
         this.chromosome = chromosome;
         this.start = start;
         this.end = end;
-        this.reference = reference;
-        this.alternate = alternate;
+        this.reference = reference.toUpperCase();
+        this.alternate = alternate.toUpperCase();
         transformToEnsemblFormat();
     }
 

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/model/PopulationStatistics.java b/src/main/java/uk/ac/ebi/eva/pipeline/model/PopulationStatistics.java
@@ -25,6 +25,7 @@
 import uk.ac.ebi.eva.pipeline.Application;
 
 import java.util.Map;
+import java.util.Objects;
 
 /**
  * Statistics related to a set of samples for a given variant.
@@ -122,15 +123,15 @@ public String getReference() {
     }
 
     void setReference(String reference) {
-        this.reference = reference;
+        this.reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
     }
 
     public String getAlternate() {
         return alternate;
     }
 
     void setAlternate(String alternate) {
-        this.alternate = alternate;
+        this.alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
     }
 
     public String getCohortId() {

diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantSourceEntryTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantSourceEntryTest.java
@@ -0,0 +1,14 @@
+package uk.ac.ebi.eva.commons.models.data;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class VariantSourceEntryTest {
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        VariantSourceEntry variantSourceEntry = new VariantSourceEntry(null, null, new String[]{"a", "t"}, null);
+        assertEquals("A", variantSourceEntry.getSecondaryAlternates()[0]);
+        assertEquals("T", variantSourceEntry.getSecondaryAlternates()[1]);
+    }
+}
diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantStatsTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantStatsTest.java
@@ -0,0 +1,14 @@
+package uk.ac.ebi.eva.commons.models.data;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class VariantStatsTest {
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        VariantStats variantStats = new VariantStats("a", "t", null);
+        assertEquals("A", variantStats.getRefAllele());
+        assertEquals("T", variantStats.getAltAllele());
+    }
+}
diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/data/VariantTest.java
@@ -0,0 +1,14 @@
+package uk.ac.ebi.eva.commons.models.data;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class VariantTest {
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        Variant variant = new Variant("1", 1, 1, "c", "t");
+        assertEquals("C", variant.getReference());
+        assertEquals("T", variant.getAlternate());
+    }
+}
diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/mongo/AnnotationTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/mongo/AnnotationTest.java
@@ -0,0 +1,16 @@
+package uk.ac.ebi.eva.commons.models.mongo;
+
+import org.junit.Test;
+import uk.ac.ebi.eva.commons.models.mongo.entity.Annotation;
+
+import static org.junit.Assert.assertEquals;
+
+public class AnnotationTest {
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        Annotation annotation = new Annotation("chr", 1, 1, "a", "t",
+                "vep", "vep_cache");
+        assertEquals("chr_1_A_T_vep_vep_cache", annotation.getId());
+    }
+}
diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/mongo/VariantDocumentTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/mongo/VariantDocumentTest.java
@@ -0,0 +1,22 @@
+package uk.ac.ebi.eva.commons.models.mongo;
+
+import org.junit.Test;
+import uk.ac.ebi.eva.commons.models.data.Variant;
+import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
+
+import java.util.Map;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+
+public class VariantDocumentTest {
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        VariantDocument variantDocument = new VariantDocument(Variant.VariantType.SNV, "chr", 1,
+                2, 1, "a", "t", (Map<String, Set<String>>) null,
+                null, null);
+
+        assertEquals("A", variantDocument.getReference());
+        assertEquals("T", variantDocument.getAlternate());
+    }
+}
diff --git a/src/test/java/uk/ac/ebi/eva/commons/models/mongo/projections/SimplifiedVariantTest.java b/src/test/java/uk/ac/ebi/eva/commons/models/mongo/projections/SimplifiedVariantTest.java
@@ -0,0 +1,21 @@
+package uk.ac.ebi.eva.commons.models.mongo.projections;
+
+import org.junit.Test;
+import uk.ac.ebi.eva.commons.models.data.Variant;
+import uk.ac.ebi.eva.commons.models.mongo.entity.projections.SimplifiedVariant;
+
+import java.util.HashMap;
+
+import static org.junit.Assert.assertEquals;
+
+public class SimplifiedVariantTest {
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        SimplifiedVariant simplifiedVariant = new SimplifiedVariant(Variant.VariantType.SNV, "chr",
+                1, 2, 1, "a", "t", new HashMap<>());
+        assertEquals("A", simplifiedVariant.getReference());
+        assertEquals("T", simplifiedVariant.getAlternate());
+    }
+
+}