Fixed type for variant in case when ref==alt (for pileup mode).

Author: PolinaBevad

src/main/java/com/astrazeneca/vardict/postprocessmodules/AmpliconPostProcessModule.java

@@ -164,8 +164,10 @@ public void process(Region rg, List<Map<Integer, Vars>> vars,
                             if (goodmap.contains(format("%s-%s-%s", amp, vref.refallele, vref.varallele))) {
                                 continue;
                             }
+                            if (instance().conf.doPileup && vref.refallele.equals(vref.varallele)) {
+                                continue;
+                            }
                             if (vref.startPosition >= reg.insertStart && vref.endPosition <= reg.insertEnd) {
-
                                 String regStr = reg.chr + ":" + reg.start + "-" + reg.end;
 
                                 if (vars.get(amp).containsKey(position) && vars.get(amp).get(position).variants.size() > 0) {

src/main/java/com/astrazeneca/vardict/variations/Variant.java

@@ -291,7 +291,9 @@ private StringBuilder debugVariantsContent(String n) {
      */
     public String varType() {
         Matcher mm = ANY_SV.matcher(varallele);
-        if (refallele.length() == 1 && varallele.length() == 1) {
+        if (refallele.equals(varallele) && refallele.length() == 1) {
+            return "";
+        } else if (refallele.length() == 1 && varallele.length() == 1) {
             return "SNV";
         } else if (mm.find()) {
             return mm.group(1);