static void bigBedClick(char *fileName, struct trackDb *tdb, char *item, int start, int end, int bedSize) /* Handle click in generic bigBed track. */ { boolean showUrl = FALSE; char *chrom = cartString(cart, "c"); /* Open BigWig file and get interval list. */ struct bbiFile *bbi = bigBedFileOpen(fileName); struct lm *lm = lmInit(0); int ivStart = start, ivEnd = end; if (start == end) { // item is an insertion; expand the search range from 0 bases to 2 so we catch it: ivStart = max(0, start-1); ivEnd++; } struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm); /* Get bedSize if it's not already defined. */ if (bedSize == 0) { bedSize = bbi->definedFieldCount; showUrl = TRUE; } char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL); int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); /* Find particular item in list - matching start, and item if possible. */ boolean found = FALSE; boolean firstTime = TRUE; struct bigBedInterval *bb; for (bb = bbList; bb != NULL; bb = bb->next) { if (!(bb->start == start && bb->end == end)) continue; if (bedSize > 3) { char *name = cloneFirstWordByTab(bb->rest); boolean match = sameString(name, item); freez(&name); if (!match) continue; } found = TRUE; if (firstTime) printf("<BR>\n"); int seq1Seq2Fields = 0; // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign) boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2"); if (seq1Seq2 && bedSize == 6) seq1Seq2Fields = 2; char *fields[bedSize+seq1Seq2Fields]; char startBuf[16], endBuf[16]; char *rest = cloneString(bb->rest); int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bedSize+seq1Seq2Fields); if (bbFieldCount != bedSize+seq1Seq2Fields) { errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)", bedSize, fileName, bbFieldCount); } struct bed *bed = bedLoadN(fields, bedSize); if (bedSize >= 6 && scoreFilter && bed->score < minScore) continue; if (showUrl && (bedSize >= 4)) printCustomUrl(tdb, item, TRUE); bedPrintPos(bed, bedSize, tdb); // display seq1 and seq2 if (seq1Seq2 && bedSize+seq1Seq2Fields == 8) printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>" "<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]); else if (isNotEmpty(rest)) { char *restFields[256]; int restCount = chopTabs(rest, restFields); int restBedFields = bedSize - 3; if (restCount > restBedFields) { if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields)) { int i; char label[20]; safef(label, sizeof(label), "nonBedFieldsLabel"); printf("<B>%s </B>", trackDbSettingOrDefault(tdb, label, "Non-BED fields:")); for (i = restBedFields; i < restCount; i++) printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]); printf("<BR>\n"); } } } if (isCustomTrack(tdb->track)) { time_t timep = bbiUpdateTime(bbi); printBbiUpdateTime(&timep); } } if (!found) { printf("No item %s starting at %d\n", emptyForNull(item), start); } lmCleanup(&lm); bbiFileClose(&bbi); }
void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct) /* Generic expression ratio deatils using microarrayGroups.ra file */ /* and not the expRecord tables. */ { char *expScale = trackDbRequiredSetting(tdb, "expScale"); char *expStep = trackDbRequiredSetting(tdb, "expStep"); double maxScore = atof(expScale); double stepSize = atof(expStep); struct bed *bedList; char *itemName = cgiUsualString("i2","none"); char *expName = (item == NULL) ? itemName : item; char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen"); char *colorVal = NULL; enum expColorType colorScheme; char colorVarName[256]; safef(colorVarName, sizeof(colorVarName), "%s.color", tdb->track); colorVal = cartUsualString(cart, colorVarName, tdbSetting); colorScheme = getExpColorType(colorVal); if (sameWord(tdb->grp, "cancerGenomics")) { /* set global flag */ isCancerGenomicsTrack = TRUE; } if (!ct) { genericHeader(tdb, itemName); bedList = loadMsBed(tdb, tdb->table, seqName, winStart, winEnd); } else if (ct->dbTrack) { genericHeader(tdb, itemName); printCustomUrl(tdb, itemName, TRUE); bedList = ctLoadMultScoresBedDb(ct, seqName, winStart, winEnd); } else bedList = bedFilterListInRange(ct->bedList, NULL, seqName, winStart, winEnd); if (bedList == NULL) printf("<b>No Expression Data in this Range.</b>\n"); else if (expName && sameString(expName, "zoomInMore")) printf("<b>Too much data to display in detail in this range.</b>\n"); else { struct microarrayGroups *groupings = NULL; struct maGrouping *combineGroup; struct hash *erHash = newHash(6); int i; if (!ct) { groupings = maGetTrackGroupings(database, tdb); combineGroup = maCombineGroupingFromCart(groupings, cart, tdb->track); } else combineGroup = maGetGroupingFromCt(ct); maBedClumpGivenGrouping(bedList, combineGroup); for (i = 0; i < combineGroup->numGroups; i++) { /* make stupid exprecord hash.perhaps eventually this won't be needed */ char id[16]; struct expRecord *er = basicExpRecord(combineGroup->names[i], i, 2); safef(id, sizeof(id), "%d", i); hashAdd(erHash, id, er); } puts("<h2></h2><p>\n"); msBedPrintTable(bedList, erHash, itemName, expName, -1*maxScore, maxScore, stepSize, 2, msBedDefaultPrintHeader, msBedExpressionPrintRow, printExprssnColorKey, getColorForExprBed, colorScheme); hashTraverseEls(erHash, erHashElFree); hashFree(&erHash); microarrayGroupsFree(&groupings); } puts("<h2></h2><p>\n"); bedFreeList(&bedList); }