Fixes pnrobinson#15 and pnrobinson#16 issues related to default/other…

… assemblies

Adds a defaultValue parameter for the assembly command line option and adds a break so hg38/GRCh38 can be identified.

src/main/java/org/monarchinitiative/omop/command/GenomicDataCommand.java

@@ -15,9 +15,10 @@
  */
 public abstract class GenomicDataCommand extends Command {
     @CommandLine.Option(names = {"-a", "--assembly"},
+            defaultValue = "hg19",
             scope = CommandLine.ScopeType.INHERIT,
-            description = "genome assembly: ${COMPLETION-CANDIDATES}, default ${DEFAULT_VALUE}")
-    protected Assembly assembly = Assembly.GRCh19;
+            description = "genome assembly: ${COMPLETION-CANDIDATES}, default ${DEFAULT-VALUE}")
+    protected Assembly assembly;
 
     @CommandLine.Option(names = "--database",
             scope = CommandLine.ScopeType.INHERIT,
@@ -53,6 +54,7 @@ protected String getJannovarPath() {
                 } else {
                     throw new Vcf2OmopRuntimeException("Could not identify databasae " + genomeDatabase);
                 }
+                break;
             default:
                 throw new Vcf2OmopRuntimeException("Could not identify assembly " + assembly.toString());
         }