a02093ad8adb1d4e964ee2d404f3b58eb0840bd1
galt
  Tue Dec 9 11:34:41 2025 -0800
hgLiftOver min match filter with -multiple fixed. It has been allowing too-small regions in the output. Error was in system since 2013. fixes #17501

diff --git src/hg/lib/liftOver.c src/hg/lib/liftOver.c
index 941a2afe144..904b64dd204 100644
--- src/hg/lib/liftOver.c
+++ src/hg/lib/liftOver.c
@@ -206,32 +206,30 @@
 verbose(2, "\n");
 for (el = list; el != NULL; el = el->next)
     {
     chain = el->val;
     if (multiple)
         {
         if (chain->qEnd - chain->qStart < minChainSizeQ ||
             chain->tEnd - chain->tStart < minChainSizeT)
                 continue;
         /* limit required match to chain range on target */
         end = min(e, chain->tEnd);
         start = max(s, chain->tStart);
         
         // see above
         if (start == end) end++;
-
-        minMatchSize = minMatch *  (end - start);
         }
     intersectSize = aliIntersectSize(chain, start, end);
     if (intersectSize >= minMatchSize)
 	slAddHead(&chainsHit, chain);
     else if (intersectSize > 0)
 	{
 	slAddHead(&chainsPartial, chain);
 	}
     else
 	{
         /* shouldn't happen ? */
 	slAddHead(&chainsMissed, chain);
 	}
     }
 slFreeList(&list);