e8c22713a73f66943a295ed2b4912e6d8069e782 braney Wed Sep 10 16:54:43 2025 -0700 allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h index 8a41d5a4464..6169d6a36f0 100644 --- src/hg/inc/quickLift.h +++ src/hg/inc/quickLift.h @@ -1,25 +1,28 @@ /* 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; @@ -50,16 +53,18 @@ /* 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 quickLiftGetChain(char *fromDb, char *toDb); /* Return the id 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(); /* 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. */ #endif