models: Add missing fields to variant_annotation.proto #TASK-7555

Author: j-coll

biodata-models/src/main/proto/protobuf/opencb/variant_annotation.proto

@@ -93,6 +93,7 @@ message ConsequenceType {
     repeated SpliceScores spliceScores = 16;
     repeated string transcriptFlags = 17;
     string source = 18;
+    repeated string acmg = 19;
 }
 
 message Repeat {
@@ -248,6 +249,12 @@ message CancerHotspotVariantAnnotation {
     string source = 10;
 }
 
+message GenomicSequenceContext {
+    int32 start = 1;
+    int32 end = 2;
+    string sequence = 3;
+}
+
 message VariantAnnotation {
     string chromosome = 1;
     int32 start = 2;
@@ -285,6 +292,8 @@ message VariantAnnotation {
     repeated GwasAssociation gwas = 30;
     repeated CancerHotspotVariantAnnotation cancer_hotspots = 31;
 
+    GenomicSequenceContext genomic_sequence_context = 32;
+
     message AdditionalAttribute {
         map<string, string> attribute = 1;
     }

biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/proto/AvroToProtoConverter.java

@@ -12,6 +12,7 @@
 import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
 public class AvroToProtoConverter {
     private final Map<String, Message.Builder> builders = new HashMap<>();
@@ -46,6 +47,10 @@ protected <Builder extends Message.Builder> Builder toProto(GenericRecord record
             logger.warn("Number of fields mismatch at " + context + ": Avro fields="
                     + record.getSchema().getFields().size() + ", Proto fields=" + descriptor.getFields().size()
                     + ", missing avro fields: " + missingInAvro + ", missing proto fields: " + missingInProto);
+            logger.warn("Proto fields: "
+                    + descriptor.getFields().stream().map(Descriptors.FieldDescriptor::getJsonName).sorted().collect(Collectors.toList()));
+            logger.warn("Avro fields: "
+                    + record.getSchema().getFields().stream().map(Schema.Field::name).sorted().collect(Collectors.toList()));
             throw new IllegalArgumentException("Number of fields mismatch at " + context + ": Avro fields="
                     + record.getSchema().getFields().size() + ", Proto fields=" + descriptor.getFields().size());
         }