f4b74472e76528b7ccf72c2a38e7b110f7d603a5 braney Sat Aug 23 13:38:41 2025 -0700 more work on quickLift track hgc click diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h index 77e215023d8..b8bfd33ed1d 100644 --- src/hg/inc/quickLift.h +++ src/hg/inc/quickLift.h @@ -1,62 +1,66 @@ /* 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" 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 otherCount; +unsigned otherBaseCount; char * id; }; #define QUICKTYPE_INSERT 0 #define QUICKTYPE_DEL 1 #define QUICKTYPE_DOUBLE 2 #define QUICKTYPE_MISMATCH 3 #define QUICKTYPE_NOTHING 4 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 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. */ #endif