81d00f3eec6ea6978c9a71ed6a48c84a0bd0c987
braney
  Wed Apr 22 14:51:08 2026 -0700
hgFind: remap bigBed search hits from source to destination coords when the track is quickLifted. Previously a search for e.g. "BRCA2" on a quickLifted hub (hg38 tracks displayed on HG02257.pat) returned hits at hg38 chr13 coordinates; clicking the result errored with "Sorry, couldn't locate chr13:... in <dest>". Adds quickLiftLiftPos() in hg/lib/quickLift.c, which reads the source->dest liftOverChainFile and calls liftOverRemapRange. Called from bigBedIntervalListToHgPositions in hg/lib/bigBedFind.c whenever tdb has quickLiftUrl/quickLiftDb; hits that don't map through the chain are dropped. refs #36340

diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h
index e58cbe6f930..3968cc1fb30 100644
--- src/hg/inc/quickLift.h
+++ src/hg/inc/quickLift.h
@@ -1,86 +1,93 @@
 /* quickLift genome annotations on the fly between assemblies using chain files */
 
 /* Copyright (C) 2023 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef QUICKLIFT_H      
 #define QUICKLIFT_H      
 
 #define quickLiftCartName     "hubQuickLift"
 
 #define quickLiftChainTableConfVariable      "quickLiftChainName"
 #define defaultQuickLiftChainTableName       "quickLiftChain"
 
 struct quickLiftRegions
 // store highlight information
 {
 struct quickLiftRegions *next;
 unsigned type;
 char *chrom;
 long chromStart;
 long chromEnd;
 char *bases;
 unsigned baseCount;
 char *oChrom;
 long oChromStart;
 long oChromEnd;
 char *otherBases;
 unsigned otherBaseCount;
 char * id;
 };
 
 #define QUICKTYPE_INSERT     0
 #define QUICKTYPE_DEL      1
 #define QUICKTYPE_DOUBLE     2
 #define QUICKTYPE_MISMATCH     3
 
 extern char *quickTypeStrings[];
 
 typedef struct slList *(*ItemLoader2)(char **row, int numFields);
 /* Load a bed file from an SQL query result. */
 
 struct bigBedInterval *quickLiftGetIntervals(char *instaPortFile, struct bbiFile *bbi,   char *chrom, int start, int end, struct hash **pChainHash);
 /* Return intervals from "other" species that will map to the current window.
  * These intervals are NOT YET MAPPED to the current assembly.
  */
 
 struct bed *quickLiftIntervalsToBed(struct bbiFile *bbi, struct hash *chainHash, struct bigBedInterval *bb);
 /* Using chains stored in chainHash, port a bigBedInterval from another assembly to a bed
  * on the reference.
  */
 
 struct slList *quickLiftSql(struct sqlConnection *conn, char *quickLiftFile, char *table, char *chromName, int winStart, int winEnd,  char *query, char *extraWhere, ItemLoader2 loader, int numFields, struct hash *chainHash);
 /* Load a list of items (usually beds) from another database in a region that corresponds to chromName:winStart-winEnd in the reference database.
  * Fill a hash with the chains that were used to map the desired range.  These chains will be used to map the query side items back to the reference. */
 
 unsigned quickLiftGetChainId(struct cart *, char *fromDb, char *toDb);
 /* Return the id from the quickLiftChain table for given assemblies. */
 
 char *quickLiftGetChainPath(struct cart *, char *fromDb, char *toDb);
 /* Return the path from the quickLiftChain table for given assemblies. */
 
 struct bed *quickLiftBeds(struct bed *bedList, struct hash *chainHash, boolean blocked);
 // Map a list of bedd in query coordinates to our current reference
 
 boolean quickLiftEnabled(struct cart *cart);
 /* Return TRUE if feature is available */
 
 struct quickLiftRegions *quickLiftGetRegions(char *ourDb, char *liftDb, char *quickLiftFile, char *chrom, int seqStart, int seqEnd);
 /* Figure out the highlight regions and cache them. */
 
 char *quickLiftChainTable();
 /* Return the name of the quickLiftChain table. */
 
 void quickLiftResolveTable(struct trackDb *tdb, char *trackTable, char **retTable, char **retLiftDb);
 /* Resolve the table name and liftDb for a quickLift track.  For custom tracks,
  * sets *retLiftDb to CUSTOM_TRASH and *retTable to the dbTableName setting;
  * otherwise sets *retTable to trackTable. Caller should have already set
  * *retLiftDb to trackDbSetting(tdb, "quickLiftDb"). */
 
 struct bed *quickLiftSqlLoadBeds(struct trackDb *tdb, char *trackTable, char *liftDb,
     char *chrom, int start, int end, char *extraWhere,
     ItemLoader2 loader, int numFields, boolean blocked);
 /* Load items from another assembly via quickLift SQL, map them back to the reference,
  * and return the lifted beds.  Handles custom track table resolution internally.
  * Caller provides liftDb from trackDbSetting(tdb, "quickLiftDb"). */
+
+boolean quickLiftLiftPos(char *sourceDb, char *destDb,
+    char *chrom, int start, int end,
+    char **retChrom, int *retStart, int *retEnd);
+/* Map a position from source (sourceDb) coords to destination (destDb) coords
+ * using the liftOver chain for sourceDb -> destDb.  Used to remap hgFind
+ * results from quickLifted bigBed tracks back to the destination assembly. */
 #endif