develop: VariationParser modified to adapt to new e89 variation data
@@ -315,17 +315,27 @@ public class VariationParser extends CellBaseParser {
}
private VariantType getVariantType(String reference, String alternate) {
- if (reference.length() != alternate.length()) {
+ if (reference.contains("(") || alternate.contains("(")) {
+ return checkSnv(reference, alternate);
+ } else if (reference.length() != alternate.length()) {
return VariantType.INDEL;
- } else {
- if (reference.equals("-") || alternate.equals("-")) {
+ } else if (reference.equals("-") || alternate.equals("-")) {
return VariantType.INDEL;
- } else if (reference.contains("(") || alternate.contains("(")) {
- return checkSnv(reference, alternate);
} else {
return VariantType.SNV;
}
- }
+//
+// if (reference.length() != alternate.length()) {
+// return VariantType.INDEL;
+// } else {
+// if (reference.equals("-") || alternate.equals("-")) {
+// return VariantType.INDEL;
+// } else if (reference.contains("(") || alternate.contains("(")) {
+// return checkSnv(reference, alternate);
+// } else {
+// return VariantType.SNV;
+// }
+// }
}
private VariantType checkSnv(String reference, String alternate) {
