TASK-7983 - Fix the clinical interpretation analysis tool

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java

@@ -208,6 +208,10 @@ public static DiseasePanel parsePanelApp(Path panelAppJsonFile) throws IOExcepti
 
         Map<String, Object> panelInfo = objectMapper.readValue(panelAppJsonFile.toFile(), Map.class);
 
+        return parsePanelApp(panelInfo);
+    }
+
+    public static DiseasePanel parsePanelApp(Map<String, Object> panelInfo) {
         List<DiseasePanel.PanelCategory> categories = new ArrayList<>(2);
         categories.add(new DiseasePanel.PanelCategory(String.valueOf(panelInfo.get("disease_group")), 1));
         categories.add(new DiseasePanel.PanelCategory(String.valueOf(panelInfo.get("disease_sub_group")), 2));

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java → biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringClinicalVariantCreator.java

@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.tools.clinical;
+package org.opencb.biodata.tools.clinical.tiering;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.MapUtils;
@@ -35,6 +35,7 @@
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.ConsequenceType;
 import org.opencb.biodata.models.variant.avro.SequenceOntologyTerm;
+import org.opencb.biodata.tools.clinical.ClinicalVariantCreator;
 
 import java.util.*;
 import java.util.stream.Collectors;

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringConfiguration.java

@@ -0,0 +1,58 @@
+package org.opencb.biodata.tools.clinical.tiering;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+import java.util.Map;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class TieringConfiguration {
+    private String penetrance;
+    private Map<String, Object> queries;
+    private Map<String, Map<String, Object>> tiers;
+
+    public TieringConfiguration() {
+    }
+
+    public TieringConfiguration(String penetrance, Map<String, Object> queries, Map<String, Map<String, Object>> tiers) {
+        this.penetrance = penetrance;
+        this.queries = queries;
+        this.tiers = tiers;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("TieringConfiguration{");
+        sb.append("penetrance='").append(penetrance).append('\'');
+        sb.append(", queries=").append(queries);
+        sb.append(", tiers=").append(tiers);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getPenetrance() {
+        return penetrance;
+    }
+
+    public TieringConfiguration setPenetrance(String penetrance) {
+        this.penetrance = penetrance;
+        return this;
+    }
+
+    public Map<String, Object> getQueries() {
+        return queries;
+    }
+
+    public TieringConfiguration setQueries(Map<String, Object> queries) {
+        this.queries = queries;
+        return this;
+    }
+
+    public Map<String, Map<String, Object>> getTiers() {
+        return tiers;
+    }
+
+    public TieringConfiguration setTiers(Map<String, Map<String, Object>> tiers) {
+        this.tiers = tiers;
+        return this;
+    }
+}