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/lib/customAdjacency.c src/hg/lib/customAdjacency.c index 8368c45987a..56e92826a14 100644 --- src/hg/lib/customAdjacency.c +++ src/hg/lib/customAdjacency.c @@ -1,261 +1,260 @@ #include "common.h" #include "errCatch.h" #include "hash.h" #include "linefile.h" #include "portable.h" #include "obscure.h" #include "binRange.h" #include "pipeline.h" #include "jksql.h" #include "net.h" #include "bed.h" #include "psl.h" #include "gff.h" #include "wiggle.h" #include "genePred.h" #include "trackDb.h" #include "hgConfig.h" #include "hdb.h" #include "hui.h" #include "customTrack.h" #include "customPp.h" #include "customFactory.h" #include "trashDir.h" #include "jsHelper.h" #include "encode/encodePeak.h" #include "udc.h" #include "bbiFile.h" #include "bigWig.h" #include "bigBed.h" #include "hgBam.h" #include "vcf.h" -#include "makeItemsItem.h" #include "bedDetail.h" #include "pgSnp.h" #include "regexHelper.h" #include "chromInfo.h" #include "adjacency.h" char *ctGenomeOrCurrent(struct customTrack *ct); /*** adjacency Factory - allow adjacency(personal genome SNP) custom tracks ***/ static boolean rowIsAdjacency (char **row, char *db, char *type) /* return TRUE if row looks like a adjacency row */ { return TRUE; #ifdef NOTNOW boolean isAdjacency = rowIsBed(row, 3, db); if (type != NULL && !sameWord(type, "adjacency")) return FALSE; if (!isAdjacency && type == NULL) return FALSE; else if (!isAdjacency) errAbort("Error line 1 of custom track, type is adjacency but first 3 fields are not BED"); if (!isdigit(row[4][0]) && type == NULL) return FALSE; else if (!isdigit(row[4][0])) errAbort("Error line 1 of custom track, type is adjacency but count is not an integer (%s)", row[4]); int count = atoi(row[4]); if (count < 1 && type == NULL) return FALSE; else if (count < 1) errAbort("Error line 1 of custom track, type is adjacency but count is less than 1"); char pattern[128]; /* include count in pattern */ safef(pattern, sizeof(pattern), "^[ACTG-]+(\\/[ACTG-]+){%d}$", count - 1); if (! regexMatchNoCase(row[3], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[3], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but allele is invalid %s", count, row[3]); safef(pattern, sizeof(pattern), "^[0-9]+(,[0-9]+){%d}$", count - 1); if (! regexMatchNoCase(row[5], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[5], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but frequency is invalid (%s)", count, row[5]); safef(pattern, sizeof(pattern), "^[0-9.]+(,[0-9.]+){%d}$", count - 1); if (! regexMatchNoCase(row[6], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[6], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but score is invalid (%s)", count, row[6]); /* if get here must be adjacency format */ return TRUE; #endif } static boolean sameType(char *a, char *b) /* Case-sensitive comparison of first word if multiple words, * so that we can compare types like "bed" vs. "bed 3 ." etc. * Tolerates one null input but not two. */ { if (a == NULL && b == NULL) errAbort("sameType should not be called when both inputs are NULL."); else if (a == NULL || b == NULL) return FALSE; char *aCopy = cloneString(a); char *bCopy = cloneString(b); char *aWord = firstWordInLine(aCopy); char *bWord = firstWordInLine(bCopy); boolean same = sameString(aWord, bWord); freeMem(aCopy); freeMem(bCopy); return same; } static boolean adjacencyRecognizer(struct customFactory *fac, struct customPp *cpp, char *type, struct customTrack *track) /* Return TRUE if looks like we're handling an adjacency track */ { if (type != NULL && !sameType(type, fac->name)) return FALSE; char *line = customFactoryNextRealTilTrack(cpp); if (line == NULL) return FALSE; char *dupe = cloneString(line); char *row[9+3]; int wordCount = chopLine(dupe, row); boolean isAdjacency = FALSE; if (wordCount == 9) { track->fieldCount = wordCount; char *ctDb = ctGenomeOrCurrent(track); isAdjacency = rowIsAdjacency(row, ctDb, type); } freeMem(dupe); customPpReuse(cpp, line); return (isAdjacency); } static struct pipeline *adjacencyLoaderPipe(struct customTrack *track) /* Set up pipeline that will load the adjacency into database. */ { /* running the single command: * hgLoadBed -customTrackLoader -sqlTable=loader/adjacency.sql -renameSqlTable * -trimSqlTable -notItemRgb -tmpDir=/data/tmp * -maxChromNameLength=${nameLength} customTrash tableName stdin */ struct dyString *tmpDy = dyStringNew(0); char *cmd1[] = {"loader/hgLoadBed", "-customTrackLoader", "-sqlTable=loader/adjacency.sql", "-noBin", "-renameSqlTable", "-trimSqlTable", "-notItemRgb", NULL, NULL, NULL, NULL, NULL, NULL}; char *tmpDir = cfgOptionDefault("customTracks.tmpdir", "/data/tmp"); struct stat statBuf; int index = 6; if (stat(tmpDir,&statBuf)) errAbort("can not find custom track tmp load directory: '%s'
\n" "create directory or specify in hg.conf customTracks.tmpdir", tmpDir); dyStringPrintf(tmpDy, "-tmpDir=%s", tmpDir); cmd1[index++] = dyStringCannibalize(&tmpDy); tmpDy = dyStringNew(0); dyStringPrintf(tmpDy, "-maxChromNameLength=%d", track->maxChromName); cmd1[index++] = dyStringCannibalize(&tmpDy); cmd1[index++] = CUSTOM_TRASH; cmd1[index++] = track->dbTableName; cmd1[index++] = "stdin"; assert(index <= ArraySize(cmd1)); /* the "/dev/null" file isn't actually used for anything, but it is used * in the pipeLineOpen to properly get a pipe started that isn't simply * to STDOUT which is what a NULL would do here instead of this name. * This function exits if it can't get the pipe created * The dbStderrFile will get stderr messages from hgLoadBed into the * our private error log so we can send it back to the user */ return pipelineOpen1(cmd1, pipelineWrite | pipelineNoAbort, "/dev/null", track->dbStderrFile, 0); } //struct adjacency *adjacencyLineFileLoad(char **row, struct lineFile *lf); void customFactoryCheckChromNameDb(char *genomeDb, char *word, struct lineFile *lf); void pipelineFailExit(struct customTrack *track); /* customTrackAdjacency load item */ static struct adjacency *customTrackAdjacency(char *db, char **row, struct hash *chromHash, struct lineFile *lf) /* Convert a row of strings to adjacency. */ { //struct adjacency *item = adjacencyLineFileLoad(row, lf); struct adjacency *item = adjacencyLoad(row); hashStoreName(chromHash, item->chrom); customFactoryCheckChromNameDb(db, item->chrom, lf); int chromSize = hChromSize(db, item->chrom); if (item->chromEnd > chromSize) lineFileAbort(lf, "chromEnd larger than chrom %s size (%d > %d)", item->chrom, item->chromEnd, chromSize); return item; } /* remember to set all the custom track settings necessary */ static struct customTrack *adjacencyFinish(struct customTrack *track, struct adjacency *itemList) /* Finish up adjacency tracks. */ { struct adjacency *item; char buf[50]; track->tdb->type = cloneString("adjacency"); track->dbTrackType = cloneString("adjacency"); safef(buf, sizeof(buf), "%d", track->fieldCount); ctAddToSettings(track, "fieldCount", cloneString(buf)); safef(buf, sizeof(buf), "%d", slCount(itemList)); ctAddToSettings(track, "itemCount", cloneString(buf)); safef(buf, sizeof(buf), "%s:%u-%u", itemList->chrom, itemList->chromStart, itemList->chromEnd); ctAddToSettings(track, "firstItemPos", cloneString(buf)); /* If necessary add track offsets. */ int offset = track->offset; if (offset != 0) { /* Add track offsets if any */ for (item = itemList; item != NULL; item = item->next) { item->chromStart += offset; item->chromEnd += offset; } track->offset = 0; /* so DB load later won't do this again */ hashMayRemove(track->tdb->settingsHash, "offset"); /* nor the file reader*/ } /* If necessary load database */ customFactorySetupDbTrack(track); struct pipeline *dataPipe = adjacencyLoaderPipe(track); FILE *out = pipelineFile(dataPipe); for (item = itemList; item != NULL; item = item->next) adjacencyOutput(item, out, '\t', '\n'); fflush(out); /* help see error from loader failure */ if(ferror(out) || pipelineWait(dataPipe)) pipelineFailExit(track); /* prints error and exits */ unlink(track->dbStderrFile); /* no errors, not used */ pipelineFree(&dataPipe); return track; } static struct customTrack *adjacencyLoader(struct customFactory *fac, struct hash *chromHash, struct customPp *cpp, struct customTrack *track, boolean dbRequested) /* Load up adjacency data until get next track line. */ { char *line; char *db = ctGenomeOrCurrent(track); struct adjacency *itemList = NULL; if (!dbRequested) errAbort("adjacency custom track type unavailable without custom trash database. Please set that up in your hg.conf"); while ((line = customFactoryNextRealTilTrack(cpp)) != NULL) { char *row[9]; int wordCount = chopLine(line, row); struct lineFile *lf = cpp->fileStack; lineFileExpectAtLeast(lf, track->fieldCount, wordCount); struct adjacency *item = customTrackAdjacency(db, row, chromHash, lf); slAddHead(&itemList, item); } slReverse(&itemList); return adjacencyFinish(track, itemList); } struct customFactory adjacencyFactory = /* Factory for adjacency tracks */ { NULL, "adjacency", adjacencyRecognizer, adjacencyLoader, };