1b7f07fe5eb75a017ecf0305de99e202e6156e3f markd Mon Jan 30 17:42:19 2017 -0800 fixed hgc crash on transMap V2 tracks diff --git src/hg/hgc/transMapClick.c src/hg/hgc/transMapClick.c index bc7f82e..e2b4f9c 100644 --- src/hg/hgc/transMapClick.c +++ src/hg/hgc/transMapClick.c @@ -105,47 +105,52 @@ return "rbest"; } assert(FALSE); return NULL; } static struct bigTransMap *buildFakeBigTransMapRec(struct transMapInfo *info, struct transMapSrc *src, struct transMapGene *gene) /* build a partial bigTransMap record from the tables; only metadata fields * are filled in. */ { struct bigTransMap *bigTransMap; AllocVar(bigTransMap); bigTransMap->seqType = 1; +bigTransMap->name = cloneString(src->id); bigTransMap->srcDb = cloneString(src->db); bigTransMap->srcChrom = cloneString(src->chrom); bigTransMap->srcChromStart = src->chromStart; bigTransMap->srcChromEnd = src->chromEnd; bigTransMap->srcScore = (int)(1000.0*src->ident); bigTransMap->srcAligned = (int)(1000.0*src->aligned); if (gene != NULL) { bigTransMap->geneName = cloneString(gene->geneName); bigTransMap->geneId = cloneString(gene->geneId); + bigTransMap->oCDS = cloneString(gene->cds); } bigTransMap->geneType = cloneString(guessTranscriptType(gene)); // set for ESTs bigTransMap->transcriptType = cloneString(guessTranscriptType(gene)); bigTransMap->chainType = cloneString(chainSubsetToBigStr(info->chainSubset)); bigTransMap->commonName = hOrganism(info->srcDb); if (bigTransMap->commonName == NULL) bigTransMap->commonName = cloneString(""); +bigTransMap->scientificName = hScientificName(info->srcDb); +if (bigTransMap->scientificName == NULL) + bigTransMap->scientificName = cloneString(""); bigTransMap->orgAbbrev = cloneString(emptyForNull(hOrgShortForDb(info->srcDb))); return bigTransMap; } static struct transMapBag *transMapBagLoadDb(struct trackDb *tdb, char *mappedId) /* load information from various tables for database version of transmap */ { struct sqlConnection *conn = hAllocConn(database); struct transMapBag *bag; AllocVar(bag); bag->psl = getAlignments(conn, tdb->table, mappedId); char *transMapInfoTbl = trackDbRequiredSetting(tdb, transMapInfoTblSetting); struct transMapInfo *info = transMapInfoQuery(conn, transMapInfoTbl, mappedId);