don't use the first read when we're backing up

Sergey Koren · Sergey Koren · commit f40a20407cd3 · 2023-05-10T15:37:30.000-04:00
diff --git a/src/utgcns/unitigConsensus.C b/src/utgcns/unitigConsensus.C
@@ -381,7 +381,7 @@ unitigConsensus::generateTemplateStitch(void) {
       bool   first = (nm == 0);
       bool   save  = false;
 
-      if ((nm < _utgpos[ii].max()) && (thick || first) && badToAdd.count(ii) == 0) {
+      if ((nm < _utgpos[ii].max()) && (thick || (first && !allowContains)) && badToAdd.count(ii) == 0) {
         save = true;
         nr   = ii;
         nm   = _utgpos[ii].max();
