8de67388be9a67cb94ba95615b7643b4ddc385da braney Thu Sep 24 17:48:19 2026 -0700 quickLift: give a lifted maf block the reference's own bases, refs #38249 Inside a chain block the two assemblies run in step but need not agree base for base, and the first row of a lifted block still carried the other assembly's letters. The details page showed hg19's base in the human row of a block lifted onto hg38. quickLiftMafs now reads the reference sequence once over the span of the lifted blocks and writes it into that row, leaving the gaps where they are. The lifted blocks are also sorted by position now. On a chain that turns the alignment over they came back last to first, and the details page listed them in that order. diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h index 0396747597d..8ab6d0e4285 100644 --- src/hg/inc/quickLift.h +++ src/hg/inc/quickLift.h @@ -1,176 +1,177 @@ /* 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 psl; struct chain; struct mafAli; 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 bed *quickLiftIntervalsToBedClip(struct bbiFile *bbi, struct hash *chainHash, struct bigBedInterval *bb); /* Like quickLiftIntervalsToBed, but an item too big for the chains we loaded is pulled in * to what they cover rather than dropped. Callers that need the item's true extent (the * details page) should use quickLiftIntervalsToBed instead. */ 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. */ struct genePred *quickLiftGenePreds(struct sqlConnection *conn, char *quickLiftFile, char *table, char *chromName, int winStart, int winEnd, char *extraWhere, struct hash *chainHash); /* Like quickLiftSql, but load genePreds through a genePredReader so the actual set of * (extended) genePred columns in the table is honored rather than assuming 15 columns. * Fill a hash with the chains that were used to map the desired range. */ 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 struct quickLiftRange // A range in the other assembly that some part of the reference window maps back to. { struct quickLiftRange *next; char *chrom; /* sequence name in the other assembly */ int start; int end; }; struct quickLiftRange *quickLiftSourceRanges(char *quickLiftFile, char *chrom, int start, int end, struct hash *chainHash); // The ranges in the other assembly that map into chrom:start-end on the reference. The // chains that do the mapping are added to chainHash, which is the form the lift functions // read. Use this when the items cannot be had from a query quickLiftSql knows how to make. struct hash *quickLiftChainHash(char *quickLiftFile, char *chrom, int start, int end); // Load the quickLift chains covering chrom:start-end on the reference and return them in a // hash keyed on the other assembly's sequence names, which is the shape the lift functions // want. Use this when the items were fetched some other way, so quickLiftSql was not the // thing that collected the chains. struct psl *quickLiftPsl(struct hash *chainHash, struct hash **pMapPsls, struct psl *psl); // Map the target side of an alignment from the other assembly onto our current reference. // The query side (the mRNA, EST or protein the alignment is to) is left alone. Returns // NULL if the alignment doesn't map. pMapPsls points at a hash of mapping alignments the // caller keeps across a run of items; point it at a NULL hash to start. struct mafAli *quickLiftMafs(struct hash *chainHash, struct mafAli *mafList, - char *sourceDb, char *refSrc, int refSrcSize); + char *sourceDb, char *refDb, char *refChrom, char *refSrc, int refSrcSize); // Map MAF blocks from the other assembly onto our current reference. A block is cut at // every chain block boundary, since a MAF block has to be one contiguous run on its first // row and the lift does not keep the reference contiguous. refSrc is the name the browser -// expects on the reference row, "<db>.<chrom>", with no hub prefix. +// expects on the reference row, "<db>.<chrom>", with no hub prefix. The bases on that row +// are replaced with refDb's own sequence of refChrom. boolean quickLiftIsLifted(struct trackDb *tdb); // TRUE when this track's data comes from another assembly and there is enough to lift it. // Both halves have to be there: the chain file that does the lifting and the assembly the // data came from. A hub can set either one on its own, and half the pair is no use. boolean quickLiftIsOwnChainTrack(struct trackDb *tdb); // TRUE when this is the chain track quickLift builds to show the lift itself. That stanza // carries quickLiftUrl and quickLiftDb like any lifted track, but its data is already in // reference coordinates and must not be lifted a second time. struct chain *quickLiftChain(struct hash *chainHash, struct hash **pMapPsls, struct chain *chain); // Map a chain's target side from the other assembly onto our current reference. A chain is // an alignment between that assembly and some other species, so this composes the two and // leaves a chain between the reference and that species. The query side is left alone. // Returns NULL if the chain doesn't map. The chain handed in is not modified. struct psl *quickLiftPsls(struct hash *chainHash, struct psl *pslList); // Map a list of alignments in the other assembly's coordinates onto our current reference. // Alignments that don't map are dropped. struct encodePeak *quickLiftPeaks(struct encodePeak *peakList, struct hash *chainHash); // Map a list of encodePeaks in query coordinates to our current reference. These can't go // through quickLiftBeds: the thickStart and thickEnd it assigns overlay signalValue and // pValue in struct encodePeak. boolean quickLiftEnabled(struct cart *cart); /* Return TRUE if feature is available */ boolean quickLiftAlignmentsEnabled(struct cart *cart); /* Return TRUE if quickLift is allowed to lift alignment tracks: psl, bigPsl, chain, * bigChain, maf, bigMaf and wigMaf. Off unless hg.conf says * browser.quickLiftAlignments=on, and a cart variable of the same name overrides that. */ 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. */ boolean quickLiftHubRemoveTrack(struct cart *cart, char *sourceDb, char *trackName); /* Remove a track stanza from the quickLift hub file for sourceDb. Returns * TRUE if a stanza matching trackName was found and removed. */ #endif