d972170022c5cbf6be7c1fdf31afba23d826608b
braney
  Tue Jan 20 10:33:00 2026 -0800
when quickLifting SQL genepreds be a little more forgiving of the
alignment  no RM

diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 8e585734aa4..0efe64bf5c4 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -6296,38 +6296,40 @@
         liftDb = CUSTOM_TRASH;
         table = trackDbSetting(tg->tdb, "dbTableName");
         }
     else
         table = tg->table;
     struct hash *chainHash = newHash(8);
     struct sqlConnection *conn = hAllocConn(liftDb);
     char *quickLiftFile = cloneString(trackDbSetting(tg->tdb, "quickLiftUrl"));
 
 // using this loader on genePred tables with less than 15 fields may be a problem.
 extern struct genePred *genePredExtLoad15(char **row);
 
     struct genePred *gpList = (struct genePred *)quickLiftSql(conn, quickLiftFile, table, chromName, winStart, winEnd,  NULL, NULL, (ItemLoader2)genePredExtLoad15, 0, chainHash);
     hFreeConn(&conn);
 
-    calcLiftOverGenePreds( gpList, chainHash, 0.0, 1.0, TRUE, NULL, NULL,  TRUE, FALSE);
+    calcLiftOverGenePreds( gpList, chainHash, 0.0, 0.0, TRUE, NULL, NULL,  TRUE, FALSE);
     struct genePred *gp = gpList;
 
     struct linkedFeatures *lfList = NULL;
     for(;gp; gp = gp->next)
         {
         if (gp->chrom == NULL) // if the lift failed, ignore this one
             continue;
+        if (positiveRangeIntersection(winStart, winEnd, gp->txStart, gp->txEnd) == 0)
+            continue;
         // we need to reverse the order of the exon frames if the quickLift changed the strand
         if (quickLiftFile && (gp->strand[0] != gp->origStrand) && (gp->exonCount > 1))
             {
             int *reorderFrames;
             AllocArray(reorderFrames, gp->exonCount);
 
             int ii;
             for(ii=0; ii < gp->exonCount; ii++)
                 reorderFrames[ii] = gp->exonFrames[(gp->exonCount - 1) - ii];
 
             gp->exonFrames = reorderFrames;
             }
         slAddHead(&lfList, linkedFeaturesFromGenePred(tg, gp, TRUE));
         }
     slReverse(&lfList);