dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a braney Tue Apr 22 12:26:11 2025 -0700 sessions save a copy of the quickLift hub. diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h index 52c151f0207..e7a5345f020 100644 --- src/hg/inc/quickLift.h +++ src/hg/inc/quickLift.h @@ -1,34 +1,36 @@ /* 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" + 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 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 */ #endif