d5da43405653dc8af678771414b19cac3270847b markd Wed Dec 28 15:37:24 2011 -0800 fixed missing page closes diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c index 099c211..ed41c00 100644 --- src/hg/hgc/gencodeClick.c +++ src/hg/hgc/gencodeClick.c @@ -1,654 +1,655 @@ /* gencodeClick - click handling for GENCODE tracks */ #include "common.h" #include "hgc.h" #include "gencodeClick.h" #include "genePred.h" #include "genePredReader.h" #include "ensFace.h" #include "htmshell.h" #include "jksql.h" #include "encode/wgEncodeGencodeAttrs.h" #include "encode/wgEncodeGencodeGeneSource.h" #include "encode/wgEncodeGencodePdb.h" #include "encode/wgEncodeGencodePubMed.h" #include "encode/wgEncodeGencodeRefSeq.h" #include "encode/wgEncodeGencodeTag.h" #include "encode/wgEncodeGencodeTranscriptSource.h" #include "encode/wgEncodeGencodeTranscriptSupport.h" #include "encode/wgEncodeGencodeExonSupport.h" #include "encode/wgEncodeGencodeUniProt.h" #include "encode/wgEncodeGencodeAnnotationRemark.h" /* * General notes: * - this will be integrated into hgGene at some point, however this was * done as part of hgc for timing reasons and to allow more time to design * the hgGene part. * - Tables below will output at least one row even if no data is available. * */ /* size for buffering URL strings */ static const int urlBufSize = 512; static char *getGencodeTable(struct trackDb *tdb, char *tableBase) /* get a table name from the settings. */ { return trackDbRequiredSetting(tdb, tableBase); } static int transAnnoCmp(const void *va, const void *vb) /* Compare genePreds, sorting to keep select gene first. The only cases * that annotations will be duplicated is if they are in the PAR and thus * on different chroms. */ { const struct genePred *a = *((struct genePred **)va); const struct genePred *b = *((struct genePred **)vb); if (sameString(a->name, seqName)) return -1; else if (sameString(b->name, seqName)) return 1; else return strcmp(a->name, b->name); } static struct genePred *transAnnoLoad(struct sqlConnection *conn, struct trackDb *tdb, char *gencodeId) /* load the gencode annotations and sort the one corresponding to the one that was clicked on is * first. Should only have one or two. */ { // must check chrom due to PAR char where[256]; safef(where, sizeof(where), "(chrom = \"%s\") and (name = \"%s\")", seqName, gencodeId); struct genePred *transAnno = genePredReaderLoadQuery(conn, tdb->track, where); slSort(&transAnno, transAnnoCmp); return transAnno; } static struct wgEncodeGencodeAttrs *transAttrsLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId) /* load the gencode class information */ { return sqlQueryObjs(conn, (sqlLoadFunc)wgEncodeGencodeAttrsLoad, sqlQuerySingle|sqlQueryMust, "select * from %s where transcriptId = \"%s\"", getGencodeTable(tdb, "wgEncodeGencodeAttrs"), gencodeId); } static void getGeneBounds(struct trackDb *tdb, struct sqlConnection *conn, struct genePred *transAnno, int *geneChromStart, int *geneChromEnd) /* find bounds for the gene */ { // must check chrom due to PAR char where[256]; safef(where, sizeof(where), "(chrom = \"%s\") and (name2 = \"%s\")", seqName, transAnno->name2); struct genePred *geneAnnos = genePredReaderLoadQuery(conn, tdb->track, where); struct genePred *geneAnno; *geneChromStart = transAnno->txStart; *geneChromEnd = transAnno->txEnd; for (geneAnno = geneAnnos; geneAnno != NULL; geneAnno = geneAnno->next) { *geneChromStart = min(*geneChromStart, geneAnno->txStart); *geneChromEnd = max(*geneChromEnd, transAnno->txEnd); } genePredFreeList(&geneAnnos); } static void *metaDataLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId, char *tableBase, char *keyCol, unsigned queryOpts, sqlLoadFunc loadFunc) /* load autoSql objects for gencode meta data. */ { return sqlQueryObjs(conn, loadFunc, queryOpts, "select * from %s where %s = \"%s\"", getGencodeTable(tdb, tableBase), keyCol, gencodeId); } static int uniProtDatasetCmp(const void *va, const void *vb) /* Compare wgEncodeGencodeUniProt by dateset */ { const struct wgEncodeGencodeUniProt *a = *((struct wgEncodeGencodeUniProt **)va); const struct wgEncodeGencodeUniProt *b = *((struct wgEncodeGencodeUniProt **)vb); return a->dataset - b->dataset; } static char *getMethodDesc(char *source) /* return the annotation method name based gene or transcript source */ { // looks for being havana and/or ensembl // classifies other sources as automatic (mt_genbank_import ncrna ncrna_pseudogene) bool hasHav = containsStringNoCase(source, "havana") != NULL; bool hasEns = containsStringNoCase(source, "ensembl") != NULL; if (hasHav && hasEns) return "manual & automatic"; else if (hasHav) return "manual"; else return "automatic"; } static char *getLevelDesc(int level) /* return english description for level */ { if (level == 1) return "validated"; else if (level == 2) return "manual"; else if (level == 3) return "automatic"; else return "unknown"; } static char *mkExtIdUrl(struct trackDb *tdb, char *id, char *settingName, char *urlBuf) /* generate a url to a external database given an id and the name of a setting * containing the sprintf URL template.*/ { safef(urlBuf, urlBufSize, trackDbRequiredSetting(tdb, settingName), id); return urlBuf; } static void prExtIdAnchor(struct trackDb *tdb, char *id, char *settingName) /* if an id to an external database is not empty, print an HTML anchor to it */ { char urlBuf[urlBufSize]; if (!isEmpty(id)) printf("%s", mkExtIdUrl(tdb, id, settingName, urlBuf), id); } static void prTdExtIdAnchor(struct trackDb *tdb, char *id, char *settingName) /* print a table data element with an anchor for a id */ { printf(""); prExtIdAnchor(tdb, id, settingName); } static void writePosLink(char *chrom, int chromStart, int chromEnd) /* write link to a genomic position */ { printf("%s:%d-%d", hgTracksPathAndSettings(), database, chrom, chromStart, chromEnd, chrom, chromStart+1, chromEnd); } static void writeBasicInfoHtml(struct trackDb *tdb, char *gencodeId, struct genePred *transAnno, struct wgEncodeGencodeAttrs *transAttrs, int geneChromStart, int geneChromEnd, struct wgEncodeGencodeGeneSource *geneSource, struct wgEncodeGencodeTranscriptSource *transcriptSource) /* write basic HTML info for all genes */ { /* * notes: * - According to Steve: `status' is not the same for ensembl and havana. So either avoid displaying it * or display it as `automatic status' or `manual status'. */ // basic gene and transcript information printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); // FIXME: white-space style should be in CCS, but don't want to risk breaking // other things. printf("\n"); printf("\n", transAnno->strand); printf("\n", transAttrs->transcriptType, transAttrs->geneType); /* FIXME: add href o */ printf("\n", transAttrs->transcriptStatus, transAttrs->geneStatus); printf("\n", getLevelDesc(transAttrs->level), transAttrs->level); printf("\n", getMethodDesc(transcriptSource->source), getMethodDesc(geneSource->source)); printf("\n", transAttrs->geneName); printf("\n", transAttrs->ccdsId); // FIXME: add sequence here?? printf("
TranscriptGene
Gencode id"); prTdExtIdAnchor(tdb, transAttrs->transcriptId, "ensemblTranscriptIdUrl"); prTdExtIdAnchor(tdb, transAttrs->geneId, "ensemblGeneIdUrl"); printf("
HAVANA manual id"); prTdExtIdAnchor(tdb, transAttrs->havanaTranscriptId, "vegaTranscriptIdUrl"); prTdExtIdAnchor(tdb, transAttrs->havanaGeneId, "vegaGeneIdUrl"); printf("
Position"); printf(""); writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd); printf(""); writePosLink(transAnno->chrom, geneChromStart, geneChromEnd); printf("
Strand%s
Biotype%s%s
Status%s%s
Annotation Level%s (%d)
Annotation Method%s%s
HUGO gene%s
CCDS%s
\n"); } static void writeSequenceHtml(struct trackDb *tdb, char *gencodeId, struct genePred *transAnno) /* write links to get sequences */ { printf("\n"); printf("\n"); printf("\n"); if (transAnno->cdsStart < transAnno->cdsEnd) { // protein coding printf("\n"); } else { // non-protein coding printf("\n"); } printf("
Sequences
"); hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName); printf("Predicted mRNA"); printf(""); hgcAnchorSomewhere("htcTranslatedPredMRna", gencodeId, "translate", seqName); printf("Predicted protein
"); hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName); printf("Predicted mRNA
\n"); } static void writeAnnotationRemarkHtml(struct wgEncodeGencodeAnnotationRemark *remarks) /* write HTML links to remarks */ { printf("\n"); printf("\n"); printf("\n"); struct wgEncodeGencodeAnnotationRemark *remark; for (remark = remarks; remark != NULL; remark = remark->next) { char *encRemark = htmlEncode(remark->remark); printf("\n", encRemark); freeMem(encRemark); } printf("
Annotation Remarks
%s
\n"); } static void writePdbLinkHtml(struct wgEncodeGencodePdb *pdbs) /* write HTML links to PDB */ { printf("\n"); printf("\n"); printf("\n"); struct wgEncodeGencodePdb *pdb = pdbs; int i, rowCnt = 0; while ((pdb != NULL) || (rowCnt == 0)) { printf(""); for (i = 0; i < 3; i++) { printf("\n"); rowCnt++; } printf("
Protein Data Bank
"); if (pdb != NULL) { printf("%s", pdb->pdbId, pdb->pdbId); pdb = pdb->next; } } printf("
\n"); } static void writePubMedEntry(struct wgEncodeGencodePubMed *pubMed) /* write HTML table entry for a pubMed */ { printf("pubMedId); printf("\" target=_blank>%d", pubMed->pubMedId); } static void writePubMedLinkHtml(struct wgEncodeGencodePubMed *pubMeds) /* write HTML links to PubMed */ { printf("\n"); printf("\n"); printf("\n"); struct wgEncodeGencodePubMed *pubMed = pubMeds; int i, rowCnt = 0; while ((pubMed != NULL) || (rowCnt == 0)) { printf(""); for (i = 0; i < 3; i++) { if (pubMed != NULL) { writePubMedEntry(pubMed); pubMed = pubMed->next; } else printf("\n"); rowCnt++; } printf("
PubMed
"); } printf("
\n"); } static void writeRefSeqEntry(struct wgEncodeGencodeRefSeq *refSeq) /* write HTML table entry for a RefSeq */ { printf("rnaAcc); printf("\" target=_blank>%s", refSeq->rnaAcc); printf(""); if (!isEmpty(refSeq->pepAcc)) { printf("pepAcc); printf("\" target=_blank>%s", refSeq->pepAcc); } } static void writeRefSeqLinkHtml(struct wgEncodeGencodeRefSeq *refSeqs) /* write HTML links to RefSeq */ { printf("\n"); printf("\n"); printf("\n"); printf("\n"); struct wgEncodeGencodeRefSeq *refSeq = refSeqs; int rowCnt = 0; while ((refSeq != NULL) || (rowCnt == 0)) { printf(""); if (refSeq != NULL) { writeRefSeqEntry(refSeq); refSeq = refSeq->next; } else printf("\n"); rowCnt++; } printf("
RefSeq
RNAProtein
"); printf("
\n"); } static void writeUniProtEntry(struct wgEncodeGencodeUniProt *uniProt) /* write HTML table entry for a UniProt */ { printf("%s", (uniProt->dataset == wgEncodeGencodeUniProtSwissProt) ? "SwissProt" : "TrEMBL"); printf("acc); printf("\" target=_blank>%s", uniProt->acc); printf("name); printf("\" target=_blank>%s", uniProt->name); } static void writeUniProtLinkHtml(struct wgEncodeGencodeUniProt *uniProts) /* write HTML links to UniProt */ { printf("\n"); printf("\n"); printf("\n"); printf("\n"); int i, rowCnt = 0; struct wgEncodeGencodeUniProt *uniProt = uniProts; while ((uniProt != NULL) || (rowCnt == 0)) { printf(""); for (i = 0; i < 2; i++) { if (uniProt != NULL) { writeUniProtEntry(uniProt); uniProt = uniProt->next; } else printf("\n"); rowCnt++; } printf("
UniProt
Data setAccessionNameData setAccessionName
"); } printf("
\n"); } struct supportEvid /* temporary struct for subset of supporting information displayed */ { struct supportEvid *next; char *seqId; /* sequence id (memory not owned) */ char *seqSrc; /* evidence source database (memory not owned) */ }; static int supportEvidCmp(const void *va, const void *vb) /* Compare two supportEvid objects. */ { const struct supportEvid *a = *((struct supportEvid **)va); const struct supportEvid *b = *((struct supportEvid **)vb); int diff = strcmp(a->seqSrc, b->seqSrc); if (diff == 0) diff = strcmp(a->seqId, b->seqId); return diff; } static void transcriptSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeTranscriptSupport *transcriptSupports) /* convert transcriptSupport to common structure */ { struct wgEncodeGencodeTranscriptSupport *transcriptSupport; for (transcriptSupport = transcriptSupports; transcriptSupport != NULL; transcriptSupport = transcriptSupport->next) { struct supportEvid *supportEvid; AllocVar(supportEvid); supportEvid->seqId = transcriptSupport->seqId; supportEvid->seqSrc = transcriptSupport->seqSrc; slAddHead(supportEvids, supportEvid); } } static void exonSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeExonSupport *exonSupports) /* convert exonSupport to common structure */ { struct wgEncodeGencodeExonSupport *exonSupport; for (exonSupport = exonSupports; exonSupport != NULL; exonSupport = exonSupport->next) { struct supportEvid *supportEvid; AllocVar(supportEvid); supportEvid->seqId = exonSupport->seqId; supportEvid->seqSrc = exonSupport->seqSrc; slAddHead(supportEvids, supportEvid); } } static void sortUniqSupportExidence(struct supportEvid **supportEvids) /* sort support evidence and make unique */ { struct supportEvid *supportEvid, *supportEvids2 = NULL; slSort(supportEvids, supportEvidCmp); // make unique while ((supportEvid = slPopHead(supportEvids)) != NULL) { if ((supportEvids2 == NULL) || (supportEvidCmp(&supportEvid, &supportEvids2) != 0)) slAddHead(&supportEvids2, supportEvid); else freeMem(supportEvid); } slReverse(&supportEvids2); *supportEvids = supportEvids2; } static struct supportEvid *loadSupportEvid(struct wgEncodeGencodeTranscriptSupport *transcriptSupports, struct wgEncodeGencodeExonSupport *exonSupports) /* load transcript and supporting evidence into a common structure */ { struct supportEvid *supportEvids = NULL; transcriptSupportToSupportEvid(&supportEvids, transcriptSupports); exonSupportToSupportEvid(&supportEvids, exonSupports); sortUniqSupportExidence(&supportEvids); return supportEvids; } static void writeSupportExidenceEntry(struct supportEvid *supportEvid) /* write HTML table entry for a supporting evidence */ { // FIXME: should link to sources when possible printf("%s", supportEvid->seqSrc); printf("%s", supportEvid->seqId); } static void writeSupportingEvidenceLinkHtml(struct wgEncodeGencodeTranscriptSupport *transcriptSupports, struct wgEncodeGencodeExonSupport *exonSupports) /* write HTML links to supporting evidence */ { struct supportEvid *supportEvids = loadSupportEvid(transcriptSupports, exonSupports); printf("\n"); printf("\n"); printf("\n"); printf("\n"); struct supportEvid *supportEvid = supportEvids; int i, rowCnt = 0; while ((supportEvid != NULL) || (rowCnt == 0)) { printf(""); for (i = 0; i < 2; i++) { if (supportEvid != NULL) { writeSupportExidenceEntry(supportEvid); supportEvid = supportEvid->next; } else printf("\n"); rowCnt++; } printf("
Supporting Evidence
SourceSequenceSourceSequence
"); } printf("
\n"); slFreeList(&supportEvids); } static void writeTagEntry(struct wgEncodeGencodeTag *tag) /* write HTML table entry for a Tag */ { // FIXME: link to help printf("%s", tag->tag); } static void writeTagLinkHtml(struct wgEncodeGencodeTag *tags) /* write HTML links to Tag */ { printf("\n"); printf("\n"); printf("\n"); int i, rowCnt = 0; struct wgEncodeGencodeTag *tag = tags; while ((tag != NULL) || (rowCnt == 0)) { printf(""); for (i = 0; i < 3; i++) { if (tag != NULL) { writeTagEntry(tag); tag = tag->next; } else printf("\n"); rowCnt++; } printf("
Tags
"); } printf("
\n"); } static void doGencodeGeneTrack(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *transAnno) /* Process click on a GENCODE gene annotation track. */ { struct wgEncodeGencodeAttrs *transAttrs = transAttrsLoad(tdb, conn, gencodeId); char * gencodeGeneId = transAttrs->geneId; struct wgEncodeGencodeGeneSource *geneSource = metaDataLoad(tdb, conn, gencodeGeneId, "wgEncodeGencodeGeneSource", "geneId", sqlQueryMust|sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeGeneSourceLoad); struct wgEncodeGencodeTranscriptSource *transcriptSource = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSource", "transcriptId", sqlQueryMust|sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeTranscriptSourceLoad); bool haveRemarks = (trackDbSetting(tdb, "wgEncodeGencodeAnnotationRemark") != NULL); struct wgEncodeGencodeAnnotationRemark *remarks = haveRemarks ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeAnnotationRemark", "transcriptId", 0, (sqlLoadFunc)wgEncodeGencodeAnnotationRemarkLoad) : NULL; struct wgEncodeGencodePdb *pdbs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePdb", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePdbLoad); struct wgEncodeGencodePubMed *pubMeds = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePubMed", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePubMedLoad); struct wgEncodeGencodeRefSeq *refSeqs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeRefSeq", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeRefSeqLoad); struct wgEncodeGencodeTag *tags = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTag", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTagLoad); struct wgEncodeGencodeTranscriptSupport *transcriptSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTranscriptSupportLoad); struct wgEncodeGencodeExonSupport *exonSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeExonSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeExonSupportLoad); struct wgEncodeGencodeUniProt *uniProts = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeUniProt", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeUniProtLoad); slSort(&uniProts, uniProtDatasetCmp); int geneChromStart, geneChromEnd; getGeneBounds(tdb, conn, transAnno, &geneChromStart, &geneChromEnd); char *title = "GENCODE Transcript Annotation"; char header[256]; safef(header, sizeof(header), "%s %s", title, gencodeId); if (!isEmpty(transAttrs->geneName)) safef(header, sizeof(header), "%s %s (%s)", title, gencodeId, transAttrs->geneName); else safef(header, sizeof(header), "%s %s", title, gencodeId); cartWebStart(cart, database, "%s", header); printf("

%s

\n", header); writeBasicInfoHtml(tdb, gencodeId, transAnno, transAttrs, geneChromStart, geneChromEnd, geneSource, transcriptSource); writeTagLinkHtml(tags); writeSequenceHtml(tdb, gencodeId, transAnno); if (haveRemarks) writeAnnotationRemarkHtml(remarks); writePdbLinkHtml(pdbs); writePubMedLinkHtml(pubMeds); writeRefSeqLinkHtml(refSeqs); writeUniProtLinkHtml(uniProts); writeSupportingEvidenceLinkHtml(transcriptSupports, exonSupports); wgEncodeGencodeAttrsFree(&transAttrs); wgEncodeGencodeAnnotationRemarkFreeList(&remarks); wgEncodeGencodeGeneSourceFreeList(&geneSource); wgEncodeGencodeTranscriptSourceFreeList(&transcriptSource); wgEncodeGencodePdbFreeList(&pdbs); wgEncodeGencodePubMedFreeList(&pubMeds); wgEncodeGencodeRefSeqFreeList(&refSeqs); wgEncodeGencodeTranscriptSupportFreeList(&transcriptSupports); wgEncodeGencodeExonSupportFreeList(&exonSupports); wgEncodeGencodeUniProtFreeList(&uniProts); } static void doGencodeGene2WayPseudo(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *pseudoAnno) /* Process click on a GENCODE two-way pseudogene annotation track. */ { char header[256]; safef(header, sizeof(header), "GENCODE 2-way consensus pseudogene %s", gencodeId); cartWebStart(cart, database, "%s", header); printf("

%s

\n", header); printf("Yale id: "); prExtIdAnchor(tdb, gencodeId, "yalePseudoUrl"); printf("
"); printPos(pseudoAnno->chrom, pseudoAnno->txStart, pseudoAnno->txEnd, pseudoAnno->strand, FALSE, NULL); } static void doGencodeGenePolyA(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *polyAAnno) /* Process click on a GENCODE poly-A annotation track. */ { char header[256]; safef(header, sizeof(header), "GENCODE PolyA Annotation %s (%s)", polyAAnno->name2, gencodeId); cartWebStart(cart, database, "%s", header); printf("

%s

\n", header); printf("Annotation id: %s
", gencodeId); printf("Annotation Type: %s
",polyAAnno->name2); printPos(polyAAnno->chrom, polyAAnno->txStart, polyAAnno->txEnd, polyAAnno->strand, FALSE, NULL); } void doGencodeGene(struct trackDb *tdb, char *gencodeId) /* Process click on a GENCODE annotation. */ { struct sqlConnection *conn = hAllocConn(database); struct genePred *anno = transAnnoLoad(conn, tdb, gencodeId); if (startsWith("wgEncodeGencodeBasic", tdb->track) || startsWith("wgEncodeGencodeComp", tdb->track) || startsWith("wgEncodeGencodePseudoGene", tdb->track)) doGencodeGeneTrack(tdb, gencodeId, conn, anno); else if (startsWith("wgEncodeGencode2wayConsPseudo", tdb->track)) doGencodeGene2WayPseudo(tdb, gencodeId, conn, anno); else if (startsWith("wgEncodeGencodePolya", tdb->track)) doGencodeGenePolyA(tdb, gencodeId, conn, anno); else errAbort("doGencodeGene: track not handled: \"%s\"", tdb->track); htmlHorizontalLine(); printTrackHtml(tdb); +cartWebEnd(); genePredFreeList(&anno); hFreeConn(&conn); } bool isNewGencodeGene(struct trackDb *tdb) /* is this a new-style gencode (>= V7) track, as indicated by * the presence of the wgEncodeGencodeVersion setting */ { return trackDbSetting(tdb, "wgEncodeGencodeVersion") != NULL; }