remove unused data types
@@ -125,27 +125,27 @@ public class BuildCommandExecutor extends CommandExecutor {
case EtlCommons.GENE_DATA:
parser = buildGene();
break;
- case EtlCommons.VARIATION_FUNCTIONAL_SCORE_DATA:
- parser = buildCadd();
- break;
+// case EtlCommons.VARIATION_FUNCTIONAL_SCORE_DATA:
+// parser = buildCadd();
+// break;
case EtlCommons.REGULATION_DATA:
parser = buildRegulation();
break;
case EtlCommons.PROTEIN_DATA:
parser = buildProtein();
break;
- case EtlCommons.PPI_DATA:
- parser = getInteractionParser();
- break;
+// case EtlCommons.PPI_DATA:
+// parser = getInteractionParser();
+// break;
case EtlCommons.CONSERVATION_DATA:
parser = buildConservation();
break;
case EtlCommons.CLINICAL_VARIANTS_DATA:
parser = buildClinicalVariants();
break;
- case EtlCommons.STRUCTURAL_VARIANTS_DATA:
- parser = buildStructuralVariants();
- break;
+// case EtlCommons.STRUCTURAL_VARIANTS_DATA:
+// parser = buildStructuralVariants();
+// break;
case EtlCommons.REPEATS_DATA:
parser = buildRepeats();
break;
@@ -174,6 +174,7 @@ public class BuildCommandExecutor extends CommandExecutor {
}
}
+ @Deprecated
private CellBaseBuilder buildStructuralVariants() {
Path structuralVariantsFolder = downloadFolder.resolve(EtlCommons.STRUCTURAL_VARIANTS_FOLDER);
copyVersionFiles(Arrays.asList(structuralVariantsFolder.resolve(EtlCommons.DGV_VERSION_FILE)));
@@ -262,6 +263,7 @@ public class BuildCommandExecutor extends CommandExecutor {
return new GeneBuilder(geneFolderPath, genomeFastaFilePath, speciesConfiguration, flexibleGTFParsing, serializer);
}
+ @Deprecated
private CellBaseBuilder buildCadd() {
Path variationFunctionalScorePath = downloadFolder.resolve("variation_functional_score");
copyVersionFiles(Arrays.asList(variationFunctionalScorePath.resolve("caddVersion.json")));
