diff --git a/src/main/java/org/monarchinitiative/omop/command/GenomicDataCommand.java b/src/main/java/org/monarchinitiative/omop/command/GenomicDataCommand.java index 9090726..0fd93bd 100644 --- a/src/main/java/org/monarchinitiative/omop/command/GenomicDataCommand.java +++ b/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()); }