fix order

dellytools · Sep 20, 2023 · 4cd8012 · 4cd8012
1 parent 1c34a9f
commit 4cd8012
Showing 1 changed file with 13 additions and 12 deletions.
diff --git a/src/split.h b/src/split.h
@@ -687,18 +687,6 @@ namespace torali
     if (!_coordTransform(c, svRefStr, bp, ad, finalGapStart, finalGapEnd, sv.svt)) return false;
 
     if ((_translocation(sv.svt)) || (finalGapStart < finalGapEnd)) {
-      sv.precise=true;
-      sv.svStart=finalGapStart;
-      sv.svEnd=finalGapEnd;
-      sv.srAlignQuality = ad.percId;
-      sv.insLen=ad.cEnd - ad.cStart - 1;
-      sv.consBp = ad.cStart;
-      sv.homLen=std::max(0, ad.homLeft + ad.homRight - 2);
-      int32_t ci_wiggle = std::max(ad.homLeft, ad.homRight);
-      sv.ciposlow = -ci_wiggle;
-      sv.ciposhigh = ci_wiggle;
-      sv.ciendlow = -ci_wiggle;
-      sv.ciendhigh = ci_wiggle;
 
       // Get exact alleles for INS and DEL
       if (sv.svEnd - sv.svStart <= c.indelsize) {
@@ -721,6 +709,19 @@ namespace torali
 	  sv.alleles = _addAlleles(refVCF, altVCF);
 	}
       }	  
+
+      sv.precise=true;
+      sv.svStart=finalGapStart;
+      sv.svEnd=finalGapEnd;
+      sv.srAlignQuality = ad.percId;
+      sv.insLen=ad.cEnd - ad.cStart - 1;
+      sv.consBp = ad.cStart;
+      sv.homLen=std::max(0, ad.homLeft + ad.homRight - 2);
+      int32_t ci_wiggle = std::max(ad.homLeft, ad.homRight);
+      sv.ciposlow = -ci_wiggle;
+      sv.ciposhigh = ci_wiggle;
+      sv.ciendlow = -ci_wiggle;
+      sv.ciendhigh = ci_wiggle;
       return true;
     } else {
       return false;