models: Remove hgvs from Variant model. #179

opencb · Mar 20, 2020 · 93591c2 · 93591c2
1 parent c97f2bf
commit 93591c2
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Showing 7 changed files with 5 additions and 42 deletions.
diff --git a/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -19,8 +19,6 @@
 
 package org.opencb.biodata.formats.variant.annotation.io;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.MapperFeature;
 import org.codehaus.jackson.map.ObjectMapper;
 import org.junit.Test;
 import org.mortbay.util.ajax.JSON;
@@ -33,7 +31,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Created by fjlopez on 31/01/17.

diff --git a/biodata-formats/src/test/resources/variant-test.json.gz b/biodata-formats/src/test/resources/variant-test.json.gz
diff --git a/biodata-models/src/main/avro/variant.avdl b/biodata-models/src/main/avro/variant.avdl
@@ -403,11 +403,6 @@ protocol Variants {
          */
         VariantType type;
 
-        /**
-         * Unique identifier following the HGVS nomenclature.
-         */
-        union { null, map<array<string>> } hgvs = null;
-
         /**
          * Information specific to each study the variant was read from, such as
          * samples or statistics.

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java b/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java
@@ -46,7 +46,7 @@ public class Variant implements Serializable, Comparable<Variant> {
     public static final int UNKNOWN_LENGTH = 0;
 
     public Variant() {
-        impl = new VariantAvro(null, new LinkedList<>(), "", -1, -1, "", "", "+", null, 0, null, new HashMap<>(), new LinkedList<>(), null);
+        impl = new VariantAvro(null, new LinkedList<>(), "", -1, -1, "", "", "+", null, 0, null, new LinkedList<>(), null);
     }
 
     public Variant(VariantAvro avro) {
@@ -310,14 +310,6 @@ public Variant setType(VariantType value) {
         return this;
     }
 
-    public Map<String, List<String>> getHgvs() {
-        return impl.getHgvs();
-    }
-
-    public void setHgvs(Map<String, List<String>> value) {
-        impl.setHgvs(value);
-    }
-
     public VariantAnnotation getAnnotation() {
         return impl.getAnnotation();
     }
@@ -326,18 +318,6 @@ public void setAnnotation(VariantAnnotation value) {
         impl.setAnnotation(value);
     }
 
-    public boolean addHgvs(String type, String value) {
-        List<String> listByType = getHgvs().get(type);
-        if (listByType == null) {
-            listByType = new LinkedList<>();
-        }
-        if (!listByType.contains(value)) {
-            return listByType.add(value);
-        } else {
-            return false; //Collection has not changed
-        }
-    }
-
     public List<StudyEntry> getStudies() {
         return getStudiesMap() == null ? null : Collections.unmodifiableList(new ArrayList<>(getStudiesMap().values()));
     }

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/variant/VariantBuilder.java b/biodata-models/src/main/java/org/opencb/biodata/models/variant/VariantBuilder.java
@@ -509,8 +509,7 @@ protected static VariantAvro buildAvroVariant(String chromosome, int start, Inte
             int length = VariantBuilder.inferLength(reference, alternate, start, end, type);
             return new VariantAvro(null,
                     new ArrayList<>(),
-                    chromosome, start, end, reference, alternate, "+", null, length, type,
-                    new HashMap<>(), null, null);
+                    chromosome, start, end, reference, alternate, "+", null, length, type, null, null);
         }
     }
 
@@ -1096,7 +1095,7 @@ public void inferSV() {
                 case CNV:
                     Integer copyNumber = getCopyNumberFromAlternate(alternates.get(0));
                     if (copyNumber == null) {
-                        copyNumber = getCopyNumberFromFormat();
+                        copyNumber = getCopyNumberFromSampleData();
                     }
                     if (copyNumber != null) {
                         sv.setCopyNumber(copyNumber);
@@ -1198,7 +1197,7 @@ public static Integer getCopyNumberFromAlternate(String alternate) {
         }
     }
 
-    public Integer getCopyNumberFromFormat() {
+    public Integer getCopyNumberFromSampleData() {
         if (sampleDataKeys == null) {
             return null;
         }

diff --git a/biodata-models/src/main/proto/protobuf/opencb/variant.proto b/biodata-models/src/main/proto/protobuf/opencb/variant.proto
@@ -314,14 +314,6 @@ message Variant {
      */
     VariantType type = 9;
 
-    /**
-     * Unique identifier following the HGVS nomenclature.
-     */
-    message HgvsEntry {
-        repeated string info = 1;
-    }
-    map<string, HgvsEntry> hgvss = 10;
-
     /**
      * Information specific to each study the variant was read from, such as
      * samples or statistics.

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/simulator/VariantSimulator.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/simulator/VariantSimulator.java
@@ -144,7 +144,6 @@ private Variant _create(int numSamples, List<Region> regions) {
         variant.setStrand(strand);
         variant.setType(VariantType.valueOf(variantType));
         variant.setAnnotation(null);
-        variant.setHgvs(null);
         return variant;
     }