void intersectOnChrom(char *db, struct sqlConnection *conn, char *chrom, char *track1, char *track2) /* Do intersection on one chromosome. */ { int chromSize = hChromSize(chrom); struct lm *lm = lmInit(0); struct bed *bedList1, *bedList2, *andBed; struct featureBits *fb1, *fb2; Bits *bit1, *bit2; int fieldCount1, fieldCount2; struct binKeeper *bk2; uglyTime(NULL); scanChromTable(conn, chrom, track1); scanChromTable(conn, chrom, track2); uglyTime("Scan tracks"); bedList1 = getChromAsBed(conn, db, track1, chrom, lm, &fieldCount1); bedList2 = getChromAsBed(conn, db, track2, chrom, lm, &fieldCount2); uglyTime("Tracks as bed"); uglyf("%d items with %d fields in %s, ", slCount(bedList1), fieldCount1, track1); uglyf("%d items with %d fields in %s\n", slCount(bedList2), fieldCount2, track2); bit1 = bitAlloc(chromSize+8); bit2 = bitAlloc(chromSize+8); uglyTime("bitAlloc"); fb1 = fbList(db, chrom, track1, bedList1, chromSize); fb2 = fbList(db, chrom, track1, bedList1, chromSize); uglyTime("bed to featureBits list"); fbOrBits(bit1, chromSize, fb1, 0); fbOrBits(bit2, chromSize, fb2, 0); uglyTime("or into bits"); bitAnd(bit1, bit2, chromSize); uglyTime("Anding bitfields"); andBed = bitsToBed4List(bit1, chromSize, chrom, 0, 0, chromSize, lm); uglyTime("Converting bitfield to bed 4"); bitCountAllOverlaps(bedList1, bit2, fieldCount2); uglyTime("Counting overlaps in track1 with bitfield of track2"); bk2 = fbToBinKeeper(fb2, chromSize); uglyTime("Adding featureBits list from track 2 into binKeeper."); bkCountAllOverlaps(bedList1, bk2, fieldCount2); uglyTime("Count overlaps in track1 with binKeeper of track2"); featureBitsFreeList(&fb1); featureBitsFreeList(&fb2); uglyTime("free featureBits"); bitFree(&bit1); bitFree(&bit2); uglyTime("bitFree"); }
void chromFeatureSeq(struct sqlConnection *conn, char *database, char *chrom, char *trackSpec, FILE *bedFile, FILE *faFile, int *retItemCount, int *retBaseCount) /* Write out sequence file for features from one chromosome. * This separate routine handles the non-merged case. It's * reason for being is so that the feature names get preserved. */ { boolean hasBin; char t[512], *s = NULL; char table[HDB_MAX_TABLE_STRING]; struct featureBits *fbList = NULL, *fb; if (trackSpec[0] == '!') errAbort("Sorry, '!' not available with fa output unless you use faMerge"); isolateTrackPartOfSpec(trackSpec, t); s = strchr(t, '.'); if (s != NULL) errAbort("Sorry, only database (not file) tracks allowed with " "fa output unless you use faMerge"); // ignore isSplit return from hFindSplitTable() (void) hFindSplitTable(database, chrom, t, table, &hasBin); fbList = fbGetRangeQuery(database, trackSpec, chrom, 0, hChromSize(database, chrom), where, TRUE, TRUE); for (fb = fbList; fb != NULL; fb = fb->next) { int s = fb->start, e = fb->end; if (bedFile != NULL) { fprintf(bedFile, "%s\t%d\t%d\t%s", fb->chrom, fb->start, fb->end, fb->name); if (fb->strand != '?') fprintf(bedFile, "\t0\t%c", fb->strand); fprintf(bedFile, "\n"); } if (faFile != NULL) { struct dnaSeq *seq = hDnaFromSeq(database, chrom, s, e, dnaLower); if (fb->strand == '-') reverseComplement(seq->dna, seq->size); faWriteNext(faFile, fb->name, seq->dna, seq->size); freeDnaSeq(&seq); } } featureBitsFreeList(&fbList); }
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt, boolean doCtFile, boolean redirectToGb) /* Actually output bed or custom track. Return TRUE unless no results. */ { char *db = cloneString(database); char *table = curTable; struct hTableInfo *hti = getHti(db, table, conn); struct featureBits *fbList = NULL, *fbPtr; struct customTrack *ctNew = NULL; boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE) || doCt || doCtFile); char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData); char *fbQual = fbOptionsToQualifier(); char fbTQ[128]; int fields = hTableInfoBedFieldCount(hti); boolean gotResults = FALSE; struct region *region, *regionList = getRegions(); boolean isBedGr = isBedGraph(curTable); boolean isBgWg = isBigWigTable(curTable); boolean needSubtrackMerge = anySubtrackMerge(database, curTable); boolean doDataPoints = FALSE; boolean isWig = isWiggle(database, table); struct wigAsciiData *wigDataList = NULL; struct dataVector *dataVectorList = NULL; boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable)); if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt) { textOpen(); } if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) fputs("#", stdout); if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType)) doDataPoints = TRUE; for (region = regionList; region != NULL; region = region->next) { struct bed *bedList = NULL, *bed; struct lm *lm = lmInit(64*1024); struct dataVector *dv = NULL; if (isWig && doDataPoints) { if (needSubtrackMerge) { dv = wiggleDataVector(curTrack, curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else { int count = 0; struct wigAsciiData *wigData = NULL; struct wigAsciiData *asciiData; struct wigAsciiData *next; wigData = getWiggleAsData(conn, curTable, region); for (asciiData = wigData; asciiData; asciiData = next) { next = asciiData->next; if (asciiData->count) { slAddHead(&wigDataList, asciiData); ++count; } } slReverse(&wigDataList); } } else if (isBedGr && doDataPoints) { dv = bedGraphDataVector(curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else if (isBgWg && doDataPoints) { dv = bigWigDataVector(curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else if (isWig || isBgWg) { dv = wiggleDataVector(curTrack, curTable, conn, region); bedList = dataVectorToBedList(dv); dataVectorFree(&dv); } else if (isBedGr) { bedList = getBedGraphAsBed(conn, curTable, region); } else { bedList = cookedBedList(conn, curTable, region, lm, &fields); } /* this is a one-time only initial creation of the custom track * structure to receive the results. gotResults turns it off after * the first time. */ if (doCtHdr && !gotResults && ((bedList != NULL) || (wigDataList != NULL) || (dataVectorList != NULL))) { ctNew = beginCustomTrack(table, fields, doCt, (isWig || isBedGr || isBgWg), doDataPoints); } if (doDataPoints && (wigDataList || dataVectorList)) gotResults = TRUE; else { if ((fbQual == NULL) || (fbQual[0] == 0)) { for (bed = bedList; bed != NULL; bed = bed->next) { if (bed->name != NULL) { subChar(bed->name, ' ', '_'); } if (doCt) { struct bed *dupe = cloneBed(bed); /* Out of local memory. */ slAddHead(&ctNew->bedList, dupe); } else { if (doRgb) bedTabOutNitemRgb(bed, fields, stdout); else bedTabOutN(bed, fields, stdout); } gotResults = TRUE; } } else { safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual); fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE); if (fields >= 6) fields = 6; else if (fields >= 4) fields = 4; else fields = 3; if (doCt && ctNew) { ctNew->fieldCount = fields; safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1, "bed %d", fields); } for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next) { if (fbPtr->name != NULL) { char *ptr = strchr(fbPtr->name, ' '); if (ptr != NULL) *ptr = 0; } if (doCt) { struct bed *fbBed = fbToBedOne(fbPtr); slAddHead(&ctNew->bedList, fbBed ); } else { if (fields >= 6) hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n", fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name, 0, fbPtr->strand); else if (fields >= 4) hPrintf("%s\t%d\t%d\t%s\n", fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name); else hPrintf("%s\t%d\t%d\n", fbPtr->chrom, fbPtr->start, fbPtr->end); } gotResults = TRUE; } featureBitsFreeList(&fbList); } } bedList = NULL; lmCleanup(&lm); } if (!gotResults) { hPrintf(NO_RESULTS); } else if (doCt) { int wigDataSize = 0; /* Load existing custom tracks and add this new one: */ struct customTrack *ctList = getCustomTracks(); removeNamedCustom(&ctList, ctNew->tdb->table); if (doDataPoints) { if (needSubtrackMerge || isBedGr || isBgWg) { slReverse(&dataVectorList); wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL); // TODO: see if can make prettier wig output here that // doesn't necessarily have one value per base } else { struct wiggleDataStream *wds = NULL; /* create an otherwise empty wds so we can print out the list */ wds = wiggleDataStreamNew(); wds->ascii = wigDataList; wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE); #if defined(DEBUG) /* dbg */ /* allow file readability for debug */ chmod(ctNew->wigAscii, 0666); #endif wiggleDataStreamFree(&wds); } } else slReverse(&ctNew->bedList); slAddHead(&ctList, ctNew); /* Save the custom tracks out to file (overwrite the old file): */ customTracksSaveCart(db, cart, ctList); /* Put up redirect-to-browser page. */ if (redirectToGb) { char browserUrl[256]; char headerText[512]; int redirDelay = 3; safef(browserUrl, sizeof(browserUrl), "%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database); safef(headerText, sizeof(headerText), "<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">", redirDelay, browserUrl); webStartHeader(cart, database, headerText, "Table Browser: %s %s: %s", hOrganism(database), freezeName, "get custom track"); if (doDataPoints) { hPrintf("There are %d data points in custom track. ", wigDataSize); } else { hPrintf("There are %d items in custom track. ", slCount(ctNew->bedList)); } hPrintf("You will be automatically redirected to the genome browser in\n" "%d seconds, or you can \n" "<A HREF=\"%s\">click here to continue</A>.\n", redirDelay, browserUrl); } } else if (doDataPoints) { if (needSubtrackMerge || isBedGr || isBgWg) { slReverse(&dataVectorList); dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL); } else { /* create an otherwise empty wds so we can print out the list */ struct wiggleDataStream *wds = NULL; wds = wiggleDataStreamNew(); wds->ascii = wigDataList; wds->asciiOut(wds, db, "stdout", TRUE, FALSE); wiggleDataStreamFree(&wds); } } return gotResults; }