f219460db8db952415b5201ba01df99ce4999004
braney
  Thu Sep 10 13:46:42 2026 -0700
genark: pass the liftOver accession list as an slName list, refs #38328

genarkLiftOverDbs() took a pre-quoted SQL fragment that its callers
assembled.  It now takes a struct slName list and builds the query
itself with sqlDyStringCreate, so no caller writes SQL text.
Accessions that do not start with GC are skipped, since nothing else
can match the table.  hdb.c and hgConvert.c updated for the new
signature.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/inc/genark.h src/hg/inc/genark.h
index 16587cee49e..98172ae0df8 100644
--- src/hg/inc/genark.h
+++ src/hg/inc/genark.h
@@ -110,25 +110,25 @@
 /* return the genark table name from the environment, 
  * or hg.conf, or use the default.  Cache the result */
 
 /* temporary function while the genark table is in transistion with
  * new coluns being added, July 2024.  Allows compatibility with existing
  * genark table.
  */
 int genArkColumnCount();
 /* return number of columns in genark table */
 
 boolean isGenArk(char *genome);
 /* given a genome name, see if it is in the genark table to determine
  *  yes/no this is a genark genome assembly
  */
 
-struct dbDb *genarkLiftOverDbs(char *listOfAccs);
-/* return list of dbDb structures for the genark genomes that match listOfAccs */
+struct dbDb *genarkLiftOverDbs(struct slName *accList);
+/* return list of dbDb structures for the genark genomes named in accList */
 
 struct dbDb *genarkLiftOverDb(char *acc);
 /* return dbDb structure for GC* acc */
 
 struct hash *genarkGetOrgHash();
 /* read table that maps gcAccession to UCSC org. */
 #endif /* GENARK_H */