Merge pull request #297 from PolinaBevad/fix_issue_294

Fix for REF variants in amplicon pileup mode

Author: pcingola

src/main/java/com/astrazeneca/vardict/modules/ToVarsBuilder.java

@@ -952,41 +952,17 @@ else if (deletionLength < instance().conf.SVMINLEN) {
             }
         } else if (variationsAtPos.referenceVariant != null ) {  //no variant reads are detected
             Variant vref = variationsAtPos.referenceVariant;
-            updateRefVariant(position, totalPosCoverage, vref, debugLines,
-                    referenceForwardCoverage, referenceReverseCoverage);
+            updateRefVariant(position, totalPosCoverage, vref, debugLines, referenceForwardCoverage, referenceReverseCoverage);
         } else {
             variationsAtPos.referenceVariant = new Variant();
         }
 
-        // Update reference variants if there were indels and start position were changed, so after update
-        // ref variants can be output in pileup
-        if (positionsForChangedRefVariant.contains(position) && variationsAtPos.referenceVariant != null) {
+        // Update reference variants if there were indels and start position were changed, or we work with amplicons
+        // so after update ref variants can be output in pileup
+        if (variationsAtPos.referenceVariant != null && instance().conf.doPileup &&
+                (positionsForChangedRefVariant.contains(position)|| instance().ampliconBasedCalling != null)) {
             Variant vref = variationsAtPos.referenceVariant;
-            updateRefVariant(position, totalPosCoverage, vref, debugLines,
-                    referenceForwardCoverage, referenceReverseCoverage);
-        }
-
-        if (instance().conf.doPileup && variationsAtPos.referenceVariant != null) {
-            Variant refVar = variationsAtPos.referenceVariant;
-            fillReferenceVarInPileup(position, refVar);
-        }
-    }
-
-    /**
-     * Fill reference variant fields for pileup: positions, varallele and refallele
-     * @param position current position in reference
-     * @param refVar reference Variant
-     */
-    private void fillReferenceVarInPileup(int position, Variant refVar) {
-        refVar.startPosition = position;
-        refVar.endPosition = position;
-
-        char emptyChar = 0;
-        if (refVar.refallele.equals("")) {
-            refVar.refallele = ref.getOrDefault(position, emptyChar).toString();
-        }
-        if (refVar.varallele.equals("")) {
-            refVar.varallele = ref.getOrDefault(position, emptyChar).toString();
+            updateRefVariant(position, totalPosCoverage, vref, debugLines, referenceForwardCoverage, referenceReverseCoverage);
         }
     }
 
@@ -1001,7 +977,9 @@ private void updateRefVariant(int position, int totalPosCoverage, Variant vref,
         vref.varsCountOnReverse = 0;
         vref.msi = 0;
         vref.msint = 0;
-        vref.strandBiasFlag += ";0";
+        if (vref.strandBiasFlag.indexOf(';') == -1) {
+            vref.strandBiasFlag += ";0";
+        }
         vref.shift3 = 0;
         vref.startPosition = position;
         vref.endPosition = position;

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);