fabf13fff3e3abaf7ef83c69a8c60d0142c288a1 braney Fri May 15 12:05:59 2026 -0700 fix two remaining quickLift issues on UCSC RefSeq item detail page: CCDS link routes to source assembly (with coords lifted back) so the ccdsGene handler doesn't try to open the hub-virtual db, and Get Genomic Sequence Near Gene now reads sequence from the destination assembly at the lifted exon coordinates refs #36125 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 81103698c92..2cf3b71f6cc 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -10248,47 +10248,60 @@ itemCount = getSeqForBigGene(tdb, geneName); } else { if (isHubTrack(table)) tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash); else tdb = hashFindVal(trackHash, table); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl) { itemCount = getSeqForBigGene(tdb, geneName); } else { - char constraints[256]; - sqlSafef(constraints, sizeof(constraints), "name = '%s'", geneName); - char *db = database; char *liftDb = cloneString(trackDbSetting(tdb, "quickLiftDb")); - // When quickLifted, the genePred table lives in the source assembly, - // and the click's seqName/winStart/winEnd are in destination coords; - // lift them back to source coords so hgSeqItemsInRange finds rows. - char *querySeq = seqName; - int queryStart = winStart, queryEnd = winEnd; if (liftDb != NULL) { - db = liftDb; - quickLiftLiftPos(trackHubSkipHubName(database), liftDb, - seqName, winStart, winEnd, - &querySeq, &queryStart, &queryEnd); + // Load the genePred from the source assembly and lift it to + // destination coords, so hgSeqBed reads sequence from the + // destination assembly at the lifted exon coordinates. + struct genePred *gpList = getGenePredForPosition(table, geneName); + struct bed *bedList = NULL; + struct genePred *gp; + for (gp = gpList; gp != NULL; gp = gp->next) + slAddHead(&bedList, bedFromGenePred(gp)); + slReverse(&bedList); + char rootName[HDB_MAX_TABLE_STRING]; + char parsedChrom[HDB_MAX_CHROM_STRING]; + char *bareTable = trackHubSkipHubName(table); + hParseTableName(liftDb, bareTable, rootName, parsedChrom); + struct hTableInfo *hti = hFindTableInfo(liftDb, NULL, rootName); + if (hti == NULL) + webAbort("Error", "Could not find table info for table %s (%s)", + rootName, table); + itemCount = hgSeqBed(database, hti, bedList); + bedFreeList(&bedList); + genePredFreeList(&gpList); + } + else + { + char constraints[256]; + sqlSafef(constraints, sizeof(constraints), "name = '%s'", geneName); + itemCount = hgSeqItemsInRange(database, table, seqName, winStart, winEnd, constraints); } - itemCount = hgSeqItemsInRange(db, trackHubSkipHubName(table), querySeq, queryStart, queryEnd, constraints); } } if (itemCount == 0) printf("\n# No results returned from query.\n\n"); puts("</PRE>"); } void htcTrackHtml(struct trackDb *tdb) /* Handle click to display track html */ { cartWebStart(cart, database, "%s", tdb->shortLabel); printTrackHtml(tdb); } void doViralProt(struct trackDb *tdb, char *geneName) @@ -10824,31 +10837,31 @@ struct sqlResult *sr = NULL; char **row; sqlSafef(query, sizeof(query), "select biotype, extGeneId from %s where %s", tdb->table, condStr); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Gene Type:</B> %s<BR>\n", row[0]); printf("<B>External Gene ID:</B> %s<BR>\n", row[1]); } sqlFreeResult(&sr); } else { /* print CCDS if this is not a non-coding gene */ - printCcdsForSrcDb(conn, item); + printCcdsForSrcDb(conn, tdb, item); printf("<BR>\n"); } if (hTableExists(database, "ensInfo")) { struct sqlResult *sr; char query[256], **row; struct ensInfo *info = NULL; sqlSafef(query, sizeof(query), "select * from ensInfo where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { info = ensInfoLoad(row); @@ -13120,31 +13133,31 @@ char *org = sqlQuickString(conn, query); if (org == NULL) org = cloneString("unknown"); printf("<B>Organism:</B> %s<BR>", org); char *xenoDb = hDbForSciName(org); if ((xenoDb != NULL) && hDbIsActive(xenoDb) && hTableExists(xenoDb, "refSeqAli")) { printf("<B>UCSC browser: </B> \n"); linkToOtherBrowserSearch(xenoDb, rl->mrnaAcc); printf("%s on %s (%s)</B> \n", rl->mrnaAcc, hOrganism(xenoDb), xenoDb); printf("</A><BR>"); } freeMem(org); } -void prRefGeneInfo(struct sqlConnection *conn, char *rnaName, +void prRefGeneInfo(struct sqlConnection *conn, struct trackDb *tdb, char *rnaName, char *sqlRnaName, struct refLink *rl, boolean isXeno) /* print basic details information and links for a RefGene */ { struct sqlResult *sr; char **row; char query[256]; // For quickLifted tracks the conn is on the source assembly, while the // `database` global is the destination (possibly hub_NNN_<db>, which is // not a real MySQL db). Use the conn's db for hTableExists/startsWith // checks so we don't abort on "Unknown database". char *srcDb = sqlGetDatabase(conn); int ver = gbCdnaGetVersion(conn, rl->mrnaAcc); char *cdsCmpl = NULL; printf("<td valign=top nowrap>\n"); @@ -13173,31 +13186,31 @@ if (stat != NULL) printf(" <B>Status: </B>%s", stat); } puts("<BR>"); char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc); if (desc != NULL) { printf("<B>Description:</B> "); htmlTextOut(desc); printf("<BR>\n"); } if (isXeno) prRefGeneXenoInfo(conn, rl); else - printCcdsForSrcDb(conn, rl->mrnaAcc); + printCcdsForSrcDb(conn, tdb, rl->mrnaAcc); cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName); if (cdsCmpl != NULL) { printf("<B>CDS:</B> %s<BR>", cdsCmpl); } if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); @@ -13280,61 +13293,61 @@ } sqlFreeResult(&sr); } if (startsWith("hg", srcDb)) { printf("\n"); printf("<B>AceView:</B> "); printf("<A HREF = \"https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s\" TARGET=_blank>", rl->name); printf("%s</A><BR>\n", rl->name); } prGRShortRefGene(conn, rl->name); } -void prKnownGeneInfo(struct sqlConnection *conn, char *rnaName, +void prKnownGeneInfo(struct sqlConnection *conn, struct trackDb *tdb, char *rnaName, char *sqlRnaName, struct refLink *rl) /* print basic details information and links for a Known Gene */ { struct sqlResult *sr; char **row; char query[256]; int ver = gbCdnaGetVersion(conn, rl->mrnaAcc); char *cdsCmpl = NULL; printf("<td valign=top nowrap>\n"); printf("<H2>Known Gene %s</H2>\n", rl->name); printf("<B>KnownGene:</B> <A HREF=\""); printEntrezNucleotideUrl(stdout, rl->mrnaAcc); if (ver > 0) printf("\" TARGET=_blank>%s.%d</A>", rl->mrnaAcc, ver); else printf("\" TARGET=_blank>%s</A>", rl->mrnaAcc); fflush(stdout); puts("<BR>"); char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc); if (desc != NULL) { printf("<B>Description:</B> "); htmlTextOut(desc); printf("<BR>\n"); } -printCcdsForSrcDb(conn, rl->mrnaAcc); +printCcdsForSrcDb(conn, tdb, rl->mrnaAcc); cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName); if (cdsCmpl != NULL) { printf("<B>CDS:</B> %s<BR>", cdsCmpl); } if (rl->omimId != 0) { printf("<B>OMIM:</B> <A HREF=\""); printEntrezOMIMUrl(stdout, rl->omimId); printf("\" TARGET=_blank>%d</A><BR>\n", rl->omimId); } if (rl->locusLinkId != 0) { printf("<B>Entrez Gene:</B> "); @@ -13398,31 +13411,31 @@ errAbort("Couldn't find %s in %s table - this accession may no longer be available.", rnaName, refLinkTable); rl = refLinkLoad(row); sqlFreeResult(&sr); } else { rlR.name = strdup(kgId); rlR.mrnaAcc = strdup(kgId); rlR.locusLinkId = 0; rl = &rlR; } cartWebStart(cart, database, "Known Gene"); printf("<table border=0>\n<tr>\n"); -prKnownGeneInfo(conn, rnaName, sqlRnaName, rl); +prKnownGeneInfo(conn, tdb, rnaName, sqlRnaName, rl); printf("</tr>\n</table>\n"); /* optional summary text */ summary = getRefSeqSummary(conn, kgId); if (summary != NULL) { htmlHorizontalLine(); printf("<H3>Summary of %s</H3>\n", kgId); printf("<P>%s</P>\n", summary); freeMem(summary); } htmlHorizontalLine(); /* print alignments that track was based on */ @@ -13489,31 +13502,31 @@ else { sqlSafef(query, sizeof(query), "select * from %s r, %s g where mrnaAcc = '%s' and r.mrnaAcc=g.acc and g.version='%s'", refLinkTable,gbCdnaInfoTable, sqlRnaName, version); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) { sqlFreeResult(&sr); return NULL; } rl = refLinkLoad(row); sqlFreeResult(&sr); } /* print the first section with info */ printf("<table border=0>\n<tr>\n"); -prRefGeneInfo(conn, rnaName, sqlRnaName, rl, isXeno); +prRefGeneInfo(conn, tdb, rnaName, sqlRnaName, rl, isXeno); addGeneExtra(rl->name); /* adds columns if extra info is available */ printf("</tr>\n</table>\n"); /* optional summary text */ summary = getRefSeqSummary(conn, sqlRnaName); if (summary != NULL) { htmlHorizontalLine(); printf("<H3>Summary of %s</H3>\n", rl->name); printf("<P>%s</P>\n", summary); freeMem(summary); } htmlHorizontalLine();