putting null for refseq if refseq is na

EBIvariation · Oct 28, 2022 · c986ddb · c986ddb
1 parent 2338395
commit c986ddb
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/dus/NCBIAssemblyReportReader.java b/src/main/java/uk/ac/ebi/eva/contigalias/dus/NCBIAssemblyReportReader.java
@@ -99,7 +99,11 @@ protected void parseChromosomeLine(String[] columns) {
 
         chromosomeEntity.setGenbankSequenceName(columns[0]);
         chromosomeEntity.setInsdcAccession(columns[4]);
-        chromosomeEntity.setRefseq(columns[6]);
+        if (columns[6] == null || columns[6].isEmpty() || columns[6].equals("na")) {
+            chromosomeEntity.setRefseq(null);
+        } else {
+            chromosomeEntity.setRefseq(columns[6]);
+        }
 
         if (columns.length > 8) {
             try {
@@ -133,7 +137,11 @@ protected void parseScaffoldLine(String[] columns) {
 
         scaffoldEntity.setGenbankSequenceName(columns[0]);
         scaffoldEntity.setInsdcAccession(columns[4]);
-        scaffoldEntity.setRefseq(columns[6]);
+        if (columns[6] == null || columns[6].isEmpty() || columns[6].equals("na")) {
+            scaffoldEntity.setRefseq(null);
+        } else {
+            scaffoldEntity.setRefseq(columns[6]);
+        }
 
         if (columns.length > 8) {
             try {