e146af22d6cc07a6ccca765e2befafc8d4dd1856
angie
  Tue May 5 11:32:07 2026 -0700
Fixing bugs and typos in 0750648 caught by Claude review.
The doRipples checkbox cart var was ignored and a copy-paste typo caused bp2Max to be updated with the new value for bp1Max when merging.

diff --git src/hg/hgPhyloPlace/runUsher.c src/hg/hgPhyloPlace/runUsher.c
index febad28b378..844bdbcbb77 100644
--- src/hg/hgPhyloPlace/runUsher.c
+++ src/hg/hgPhyloPlace/runUsher.c
@@ -693,33 +693,33 @@
 else
     {
     // Attempt to merge breakpoint ranges for each member of riOldList.
     for (riOld = *pRiOldList;  riOld != NULL;  riOld = riOld->next)
         {
         if (riNew->bp1Min == riOld->bp1Min && riNew->bp1Max == riOld->bp1Max)
             {
             // Only bp2 differs; merge riNew bp2 into riOld bp2
             riOld->bp2Min = min(riOld->bp2Min, riNew->bp2Min);
             riOld->bp2Max = max(riOld->bp2Max, riNew->bp2Max);
             recombinantInfoFree(pRiNew);
             success = TRUE;
             }
         else if (riNew->bp2Min == riOld->bp2Min && riNew->bp2Max == riOld->bp2Max)
             {
-            // Only bp1 differs; merge r1New bp1 into riOld bp1
+            // Only bp1 differs; merge riNew bp1 into riOld bp1
             riOld->bp1Min = min(riOld->bp1Min, riNew->bp1Min);
-            riOld->bp2Max = max(riOld->bp1Max, riNew->bp1Max);
+            riOld->bp1Max = max(riOld->bp1Max, riNew->bp1Max);
             recombinantInfoFree(pRiNew);
             success = TRUE;
             }
         if (success)
             break;
         }
     }
 return success;
 }
 
 static struct recombinantInfo *filterRecombinants(struct recombinantInfo *riList)
 /* Filter riList, which must be sorted by parsimonyImprovement, to keep at most the top 3 results
  * for each potential recombinant node (plus any subsequent results that are tied for 3rd place
  * with the same parsimony improvement). */
 {