4bb9e8caea515342ba98d3871da76cd4ec69916f chmalee Fri May 1 14:10:00 2026 -0700 Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users diff --git src/hg/hgTables/custom.c src/hg/hgTables/custom.c index 068ed7cd015..d5ba39d413b 100644 --- src/hg/hgTables/custom.c +++ src/hg/hgTables/custom.c @@ -1,651 +1,655 @@ /* custom - stuff related to custom tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "obscure.h" #include "cheapcgi.h" #include "cart.h" #include "jksql.h" #include "hdb.h" #include "trackDb.h" #include "grp.h" #include "customTrack.h" #include "hgTables.h" - +#include "myVariants.h" struct customTrack *theCtList = NULL; /* List of custom tracks. */ struct slName *browserLines = NULL; /* Browser lines in custom tracks. */ struct customTrack *getCustomTracks() /* Get custom track list. */ { //fprintf(stdout,"database %s in cart %s", database, cartString(cart, "db")); cartSetString(cart, "db", database); if (theCtList == NULL) theCtList = customTracksParseCart(database, cart, &browserLines, NULL); return(theCtList); } struct customTrack *ctLookupName(char *name) /* Lookup name in custom track list */ { return ctFind(getCustomTracks(),name); } void flushCustomTracks() /* Flush custom track list. */ { theCtList = NULL; } struct customTrack *newCt(char *ctName, char *ctDesc, int visNum, char *ctUrl, int fields) /* Make a new custom track record for the query results. */ { struct customTrack *ct; struct trackDb *tdb; char buf[256]; tdb = customTrackTdbDefault(); tdb->table = customTrackTableFromLabel(ctName); tdb->track = cloneString(tdb->table); tdb->shortLabel = ctName; tdb->longLabel = ctDesc; safef(buf, sizeof(buf), "bed %d .", fields); tdb->type = cloneString(buf); tdb->canPack = 0; tdb->visibility = visNum; tdb->url = ctUrl; AllocVar(ct); ct->tdb = tdb; ct->genomeDb = cloneString(database); ct->fieldCount = fields; ct->needsLift = FALSE; ct->fromPsl = FALSE; ct->wiggle = FALSE; ct->wigAscii = (char *)NULL; ct->wigFile = (char *)NULL; ct->wibFile = (char *)NULL; ctAddToSettings(ct, CT_UNPARSED, "true"); return ct; } struct hTableInfo *ctToHti(struct customTrack *ct) /* Create an hTableInfo from a customTrack. */ { struct hTableInfo *hti; int fieldCount = 3; if (ct == NULL) return(NULL); AllocVar(hti); hti->rootName = cloneString(ct->tdb->table); hti->isPos = TRUE; hti->isSplit = FALSE; hti->hasBin = FALSE; hti->type = cloneString(ct->tdb->type); if (sameString("pgSnp", hti->type)) fieldCount = 4; /* only 4 bed-like */ else if (sameString("barChart", hti->type)) fieldCount = 6; /* only 6 bed-like */ else if (sameString("interact", hti->type)) fieldCount = 5; /* only 5 bed-like */ else if (sameString("bedDetail", hti->type)) fieldCount = ct->fieldCount - 2; /* bed part 4-12 */ else fieldCount = ct->fieldCount; if (fieldCount >= 3) { strncpy(hti->chromField, "chrom", 32); strncpy(hti->startField, "chromStart", 32); strncpy(hti->endField, "chromEnd", 32); } if (fieldCount >= 4) { strncpy(hti->nameField, "name", 32); } if (fieldCount >= 5) { strncpy(hti->scoreField, "score", 32); } if (fieldCount >= 6) { strncpy(hti->strandField, "strand", 32); } if (fieldCount >= 8) { strncpy(hti->cdsStartField, "thickStart", 32); strncpy(hti->cdsEndField, "thickEnd", 32); hti->hasCDS = TRUE; } if (fieldCount >= 12) { strncpy(hti->countField, "blockCount", 32); strncpy(hti->startsField, "chromStarts", 32); strncpy(hti->endsSizesField, "blockSizes", 32); hti->hasBlocks = TRUE; } return(hti); } struct slName *getBedFields(int fieldCount) /* Get list of fields for bed of given size. */ { struct slName *fieldList = NULL, *field; if (fieldCount >= 3) { field = newSlName("chrom"); slAddHead(&fieldList, field); field = newSlName("chromStart"); slAddHead(&fieldList, field); field = newSlName("chromEnd"); slAddHead(&fieldList, field); } if (fieldCount >= 4) { field = newSlName("name"); slAddHead(&fieldList, field); } if (fieldCount >= 5) { field = newSlName("score"); slAddHead(&fieldList, field); } if (fieldCount >= 6) { field = newSlName("strand"); slAddHead(&fieldList, field); } if (fieldCount >= 8) { field = newSlName("thickStart"); slAddHead(&fieldList, field); field = newSlName("thickEnd"); slAddHead(&fieldList, field); } if (fieldCount >= 9) { field = newSlName("itemRgb"); slAddHead(&fieldList, field); } if (fieldCount >= 12) { field = newSlName("blockCount"); slAddHead(&fieldList, field); field = newSlName("blockSizes"); slAddHead(&fieldList, field); field = newSlName("chromStarts"); slAddHead(&fieldList, field); } if (fieldCount >= 15) { field = newSlName("expCount"); slAddHead(&fieldList, field); field = newSlName("expIds"); slAddHead(&fieldList, field); field = newSlName("expScores"); slAddHead(&fieldList, field); } slReverse(&fieldList); return fieldList; } #ifdef UNUSED static void tabBedRow(struct bed *bed, struct slName *fieldList) /* Print out named fields from bed. */ { struct slName *field; boolean needTab = FALSE; for (field = fieldList; field != NULL; field = field->next) { char *type = field->name; if (needTab) hPrintf("\t"); else needTab = TRUE; if (sameString(type, "chrom")) hPrintf("%s", bed->chrom); else if (sameString(type, "chromStart")) hPrintf("%u", bed->chromStart); else if (sameString(type, "chromEnd")) hPrintf("%u", bed->chromEnd); else if (sameString(type, "name")) hPrintf("%s", bed->name); else if (sameString(type, "score")) hPrintf("%d", bed->score); else if (sameString(type, "strand")) hPrintf("%s", bed->strand); else if (sameString(type, "thickStart")) hPrintf("%u", bed->thickStart); else if (sameString(type, "thickEnd")) hPrintf("%u", bed->thickEnd); else if (sameString(type, "itemRgb")) { int rgb = bed->itemRgb; hPrintf("%d,%d,%d", (rgb & 0xff0000) >> 16, (rgb & 0xff00) >> 8, (rgb & 0xff)); } else if (sameString(type, "blockCount")) hPrintf("%u", bed->blockCount); else if (sameString(type, "blockSizes")) { unsigned i; for (i=0; i<bed->blockCount; ++i) hPrintf("%u,", bed->blockSizes[i]); } else if (sameString(type, "chromStarts")) { unsigned i; for (i=0; i<bed->blockCount; ++i) hPrintf("%u,", bed->chromStarts[i]); } else if (sameString(type, "expCount")) hPrintf("%u", bed->expCount); else if (sameString(type, "expIds")) { unsigned i; for (i=0; i<bed->expCount; ++i) hPrintf("%u,", bed->expIds[i]); } else if (sameString(type, "expScores")) { unsigned i; for (i=0; i<bed->expCount; ++i) hPrintf("%f,", bed->expScores[i]); } else errAbort("Unrecognized bed field %s", type); } hPrintf("\n"); } #endif /* UNUSED */ static void tabBedRowFile(struct bed *bed, struct slName *fieldList, FILE *f, char outSep) /* Print out to a file named fields from bed. */ { struct slName *field; boolean needTab = FALSE; for (field = fieldList; field != NULL; field = field->next) { char *type = field->name; if (needTab) fprintf(f, "%c", outSep); else needTab = TRUE; if (outSep == ',') fputc('"', f); if (sameString(type, "chrom")) fprintf(f, "%s", bed->chrom); else if (sameString(type, "chromStart")) fprintf(f, "%u", bed->chromStart); else if (sameString(type, "chromEnd")) fprintf(f, "%u", bed->chromEnd); else if (sameString(type, "name")) fprintf(f, "%s", bed->name); else if (sameString(type, "score")) fprintf(f, "%d", bed->score); else if (sameString(type, "strand")) fprintf(f, "%s", bed->strand); else if (sameString(type, "thickStart")) fprintf(f, "%u", bed->thickStart); else if (sameString(type, "thickEnd")) fprintf(f, "%u", bed->thickEnd); else if (sameString(type, "itemRgb")) { int rgb = bed->itemRgb; fprintf(f, "%d,%d,%d", (rgb & 0xff0000) >> 16, (rgb & 0xff00) >> 8, (rgb & 0xff)); } else if (sameString(type, "blockCount")) fprintf(f, "%u", bed->blockCount); else if (sameString(type, "blockSizes")) { unsigned i; for (i=0; i<bed->blockCount; ++i) fprintf(f, "%u,", bed->blockSizes[i]); } else if (sameString(type, "chromStarts")) { unsigned i; for (i=0; i<bed->blockCount; ++i) fprintf(f, "%u,", bed->chromStarts[i]); } else if (sameString(type, "expCount")) fprintf(f, "%u", bed->expCount); else if (sameString(type, "expIds")) { unsigned i; for (i=0; i<bed->expCount; ++i) fprintf(f, "%u,", bed->expIds[i]); } else if (sameString(type, "expScores")) { unsigned i; for (i=0; i<bed->expCount; ++i) fprintf(f, "%f,", bed->expScores[i]); } else errAbort("Unrecognized bed field %s", type); if (outSep == ',') fputc('"', f); } fprintf(f, "\n"); } struct bedFilter *bedFilterForCustomTrack(char *ctName) /* If the user specified constraints, then translate them to a bedFilter. */ { struct hashEl *var, *varList = cartFindPrefix(cart, hgtaFilterVarPrefix); int prefixSize = strlen(hgtaFilterVarPrefix); struct bedFilter *bf = NULL; int *trash; for (var = varList; var != NULL; var = var->next) { char *dbTrackFieldType = cloneString(var->name + prefixSize); char *parts[4]; int partCount; partCount = chopByChar(dbTrackFieldType, '.', parts, ArraySize(parts)); if (partCount == 4 && sameString(parts[1], ctName)) { char *db = parts[0]; char *table = parts[1]; char *field = parts[2]; char *type = parts[3]; if (sameString(type, filterPatternVar)) { char *pat = cloneString(var->val); char *varName, *dd, *cmp; if (bf == NULL) AllocVar(bf); varName = filterFieldVarName(db, table, field, filterDdVar); dd = cartOptionalString(cart, varName); varName = filterFieldVarName(db, table, field, filterCmpVar); cmp = cartOptionalString(cart, varName); if (sameString("chrom", field)) cgiToStringFilter(dd, pat, &(bf->chromFilter), &(bf->chromVals), &(bf->chromInvert)); else if (sameString("chromStart", field)) cgiToIntFilter(cmp, pat, &(bf->chromStartFilter), &(bf->chromStartVals)); else if (sameString("chromEnd", field)) cgiToIntFilter(cmp, pat, &(bf->chromEndFilter), &(bf->chromEndVals)); else if (sameString("name", field)) cgiToStringFilter(dd, pat, &(bf->nameFilter), &(bf->nameVals), &(bf->nameInvert)); else if (sameString("score", field)) cgiToIntFilter(cmp, pat, &(bf->scoreFilter), &(bf->scoreVals)); else if (sameString("strand", field)) cgiToCharFilter(dd, pat, &(bf->strandFilter), &(bf->strandVals), &(bf->strandInvert)); else if (sameString("thickStart", field)) cgiToIntFilter(cmp, pat, &(bf->thickStartFilter), &(bf->thickStartVals)); else if (sameString("thickEnd", field)) cgiToIntFilter(cmp, pat, &(bf->thickEndFilter), &(bf->thickEndVals)); else if (sameString("blockCount", field)) cgiToIntFilter(cmp, pat, &(bf->blockCountFilter), &(bf->blockCountVals)); else if (sameString("chromLength", field)) cgiToIntFilter(cmp, pat, &(bf->chromLengthFilter), &(bf->chromLengthVals)); else if (sameString("thickLength", field)) cgiToIntFilter(cmp, pat, &(bf->thickLengthFilter), &(bf->thickLengthVals)); else if (sameString("compareStarts", field)) cgiToIntFilter(cmp, pat, &(bf->compareStartsFilter), &trash); else if (sameString("compareEnds", field)) cgiToIntFilter(cmp, pat, &(bf->compareEndsFilter), &trash); freez(&pat); } } } hashElFreeList(&varList); return bf; } static void customTrackFilteredBedOnRegion( struct region *region, /* Region to get data from. */ struct customTrack *ct, /* Custom track. */ struct hash *idHash, /* Hash of identifiers or NULL */ struct bedFilter *bf, /* Filter or NULL */ struct lm *lm, /* Local memory pool. */ struct bed **pBedList /* Output get's appended to this list */ ) /* Get the custom tracks passing filter on a single region. */ { struct bed *bed; if (ct->dbTrack) { int fieldCount = ct->fieldCount; char query[512]; int rowOffset; char **row; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct sqlResult *sr = NULL; sqlSafef(query, sizeof(query), "select * from %s", ct->dbTableName); sr = hRangeQuery(conn, ct->dbTableName, region->chrom, region->start, region->end, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+rowOffset, fieldCount); if ((idHash == NULL || hashLookup(idHash, bed->name)) && (bf == NULL || bedFilterOne(bf, bed))) { struct bed *copy = lmCloneBed(bed, lm); slAddHead(pBedList, copy); } } sqlFreeResult(&sr); hFreeConn(&conn); } else { for (bed = ct->bedList; bed != NULL; bed = bed->next) { if (idHash == NULL || hashLookup(idHash, bed->name)) { if (sameString(bed->chrom, region->chrom)) { if (bed->chromStart < region->end && bed->chromEnd > region->start) { if (bf == NULL || bedFilterOne(bf, bed)) { struct bed *copy = lmCloneBed(bed, lm); slAddHead(pBedList, copy); } } } } } } } struct bed *customTrackGetFilteredBeds(char *db, char *name, struct region *regionList, struct lm *lm, int *retFieldCount) /* Get list of beds from custom track of given name that are * in current regions and that pass filters. You can bedFree * this when done. */ { struct customTrack *ct = ctLookupName(name); struct bedFilter *bf = NULL; struct bed *bedList = NULL; struct hash *idHash = NULL; struct region *region; int fieldCount; if (ct == NULL) errAbort("Can't find custom track %s", name); char *type = ct->dbTrackType; -if (type != NULL && (startsWithWord("makeItems", type) || +if (type != NULL && (startsWithWord("myVariants", type) || sameWord("bedDetail", type) || sameWord("barChart", type) || sameWord("interact", type) || sameWord("bedMethyl", type) || sameWord("pgSnp", type))) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); bedList = dbGetFilteredBedsOnRegions(conn, CUSTOM_TRASH, db, ct->dbTableName, name, regionList, lm, retFieldCount); hFreeConn(&conn); fieldCount = 9; if (sameWord("bedDetail", type)) fieldCount = *retFieldCount; else if (sameWord("pgSnp", type)) fieldCount = 4; else if (sameWord("barChart", type)) fieldCount = 6; else if (sameWord("interact", type)) fieldCount = 5; else if (sameWord("bedMethyl", type)) fieldCount = 5; } else if (ct->wiggle) { struct bed *wigBedList = NULL, *bed; /* Grab filtered beds for each region. */ for (region = regionList; region != NULL; region = region->next) { wigBedList = getWiggleAsBed(NULL, name, region, NULL, NULL, lm, NULL); for (bed = wigBedList; bed != NULL; bed = bed->next) { struct bed *copy = lmCloneBed(bed, lm); slAddHead(&bedList, copy); } /*bedFree(&wigBedList); do not free local memory*/ } fieldCount = 4; } else { /* Figure out how to filter things. */ fieldCount = ct->fieldCount; bf = bedFilterForCustomTrack(name); if (ct->fieldCount > 3) idHash = identifierHash(db, name); /* Grab filtered beds for each region. */ for (region = regionList; region != NULL; region = region->next) customTrackFilteredBedOnRegion(region, ct, idHash, bf, lm, &bedList); /* clean up. */ hashFree(&idHash); slReverse(&bedList); } if (retFieldCount != NULL) *retFieldCount = fieldCount; return bedList; } static void doTabOutBedLike(struct customTrack *ct, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep) /* Print out selected fields from a bed-like custom track. If fields * is NULL, then print out all fields. */ { struct region *regionList = getRegions(), *region; struct slName *chosenFields, *field; int count = 0; if (fields == NULL) chosenFields = getBedFields(ct->fieldCount); else chosenFields = commaSepToSlNames(fields); if (f == NULL) f = stdout; fprintf(f, "#"); for (field = chosenFields; field != NULL; field = field->next) { if (field != chosenFields) fprintf(f, "%c", outSep); if (outSep == ',') fputc('"', f); fprintf(f, "%s", field->name); if (outSep == ',') fputc('"', f); } fprintf(f, "\n"); for (region = regionList; region != NULL; region = region->next) { struct lm *lm = lmInit(64*1024); struct bed *bed, *bedList = cookedBedList(conn, table, region, lm, NULL); for (bed = bedList; bed != NULL; bed = bed->next) { tabBedRowFile(bed, chosenFields, f, outSep); ++count; } lmCleanup(&lm); } if (count == 0) explainWhyNoResults(f); } void doTabOutCustomTracks(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep) /* Print out selected fields from custom track. If fields * is NULL, then print out all fields. */ { struct customTrack *ct = ctLookupName(table); char *type = ct->tdb->type; -if (startsWithWord("makeItems", type) || +if (startsWithWord("myVariants", type) || sameWord("bedDetail", type) || sameWord("barChart", type) || sameWord("interact", type) || sameWord("bedMethyl", type) || sameWord("pgSnp", type)) { + if (sameWord("myVariants", type)) + { + ct->dbTableName = myVariantsResolveDbTableForCustomTrack(ct->tdb->table, cart); + } struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); doTabOutDb(CUSTOM_TRASH, db, ct->dbTableName, table, f, conn, fields, outSep); hFreeConn(&conn); } else doTabOutBedLike(ct, table, conn, fields, f, outSep); } void removeNamedCustom(struct customTrack **pList, char *name) /* Remove named custom track from list if it's on there. */ { struct customTrack *newList = NULL, *ct, *next; for (ct = *pList; ct != NULL; ct = next) { next = ct->next; if (!sameString(ct->tdb->table, name)) { slAddHead(&newList, ct); } } slReverse(&newList); *pList = newList; } void doRemoveCustomTrack(struct sqlConnection *conn) /* Remove custom track file. */ { getCustomTracks(); if (theCtList) removeNamedCustom(&theCtList, curTable); customTracksSaveCart(database, cart, theCtList); initGroupsTracksTables(); doMainPage(conn); }