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; }
void doSummaryStatsWiggle(struct sqlConnection *conn) /* Put up page showing summary stats for wiggle track. */ { // grab the right trackDb for the current table. The curTrack variable // has the composite trackDb in it struct trackDb *track = hTrackDbForTrack(database, curTable); char *table = curTable; struct region *region, *regionList = getRegions(); char *regionName = getRegionName(); long long regionSize = 0; long long gapTotal = 0; long startTime = 0, wigFetchTime = 0; char splitTableOrFileName[HDB_MAX_TABLE_STRING]; struct customTrack *ct = NULL; boolean isCustom = FALSE; struct wiggleDataStream *wds = NULL; unsigned long long valuesMatched = 0; int regionCount = 0; int regionsDone = 0; unsigned span = 0; char *dataConstraint; double ll = 0.0; double ul = 0.0; boolean hasConstraint = FALSE; char *table2 = NULL; boolean fullGenome = FALSE; boolean statsHeaderDone = FALSE; boolean gotSome = FALSE; char *shortLabel = table; long long statsItemCount = 0; /* global accumulators for overall */ int statsSpan = 0; /* stats summary on a multiple region */ double statsSumData = 0.0; /* output */ double statsSumSquares = 0.0; /* " " */ double lowerLimit = INFINITY; /* " " */ double upperLimit = -1.0 * INFINITY; /* " " */ startTime = clock1000(); if (track != NULL) shortLabel = track->shortLabel; /* Count the regions, when only one, we can do more stats */ for (region = regionList; region != NULL; region = region->next) ++regionCount; htmlOpen("%s (%s) Wiggle Summary Statistics", shortLabel, table); if (anySubtrackMerge(database, curTable)) hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this " "page (not implemented yet). Statistics shown here are only for " "the primary table %s (%s).</EM>", shortLabel, table); fullGenome = fullGenomeRegion(); WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */ for (region = regionList; region != NULL; region = region->next) { struct bed *intersectBedList = NULL; int operations; ++regionsDone; if (table2) intersectBedList = bedTable2(conn, region, table2); operations = wigFetchStats; #if defined(NOT) /* can't do the histogram now, that operation times out */ if (1 == regionCount) operations |= wigFetchAscii; #endif wds->setChromConstraint(wds, region->chrom); if (fullGenome) wds->setPositionConstraint(wds, 0, 0); else wds->setPositionConstraint(wds, region->start, region->end); if (hasConstraint) wds->setDataConstraint(wds, dataConstraint, ll, ul); /* depending on what is coming in on regionList, we may need to be * smart about how often we call getData for these custom tracks * since that is potentially a large file read each time. */ if (isCustom) { if (ct->dbTrack) { struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH); struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName); span = minSpan(trashConn, splitTableOrFileName, region->chrom, region->start, region->end, cart, tdb); wds->setSpanConstraint(wds, span); valuesMatched = getWigglePossibleIntersection(wds, region, CUSTOM_TRASH, table2, &intersectBedList, splitTableOrFileName, operations); hFreeConn(&trashConn); } else { valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2, &intersectBedList, splitTableOrFileName, operations); /* XXX We need to properly get the smallest span for custom tracks */ /* This is not necessarily the correct answer here */ if (wds->stats) span = wds->stats->span; else span = 1; } } else { if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL)) { span = minSpan(conn, splitTableOrFileName, region->chrom, region->start, region->end, cart, track); wds->setSpanConstraint(wds, span); valuesMatched = getWigglePossibleIntersection(wds, region, database, table2, &intersectBedList, splitTableOrFileName, operations); if (intersectBedList) span = 1; } } /* when doing multiple regions, we need to print out each result as * it happens to keep the connection open to the browser and * prevent any timeout since this could take a while. * (worst case test is quality track on panTro1) */ if (wds->stats) statsItemCount += wds->stats->count; if (wds->stats && (regionCount > 1) && (valuesMatched > 0)) { double sumData = wds->stats->mean * wds->stats->count; double sumSquares; if (wds->stats->count > 1) sumSquares = (wds->stats->variance * (wds->stats->count - 1)) + ((sumData * sumData)/wds->stats->count); else sumSquares = sumData * sumData; /* global accumulators for overall summary */ statsSpan = wds->stats->span; statsSumData += sumData; statsSumSquares += sumSquares; if (wds->stats->lowerLimit < lowerLimit) lowerLimit = wds->stats->lowerLimit; if ((wds->stats->lowerLimit + wds->stats->dataRange) > upperLimit) upperLimit = wds->stats->lowerLimit + wds->stats->dataRange; if (statsHeaderDone) wds->statsOut(wds, database, "stdout", TRUE, TRUE, FALSE, TRUE); else { wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, TRUE); statsHeaderDone = TRUE; } wds->freeStats(wds); gotSome = TRUE; } if ((regionCount > MAX_REGION_DISPLAY) && (regionsDone >= MAX_REGION_DISPLAY)) { hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> Can not display more " "than %d regions, <BR> would take too much time </TH></TR>\n", MAX_REGION_DISPLAY); break; /* exit this for loop */ } } /*for (region = regionList; region != NULL; region = region->next) */ if (hasConstraint) freeMem(dataConstraint); /* been cloned into wds */ if (1 == regionCount) { statsPreamble(wds, regionList->chrom, regionList->start, regionList->end, span, valuesMatched, table2); /* 3 X TRUE = sort results, html table output, with header, * the FALSE means close the table after printing, no more rows to * come. The case in the if() statement was already taken care of * in the statsPreamble() printout. No need to do that again. */ if ( ! ((valuesMatched == 0) && table2) ) wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE); regionSize = basesInRegion(regionList,0); gapTotal = gapsInRegion(conn, regionList,0); } else { /* this is a bit of a kludge here since these printouts are done in the * library source wigDataStream.c statsOut() function and * this is a clean up of that. That function should be * pulled out of there and made independent and more * versatile. */ long long realSize; double variance; double stddev; /* Too expensive to lookup the numbers for thousands of regions */ regionSize = basesInRegion(regionList,MAX_REGION_DISPLAY); gapTotal = gapsInRegion(conn, regionList,MAX_REGION_DISPLAY); realSize = regionSize - gapTotal; /* close the table which was left open in the loop above */ if (!gotSome) hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> No data found matching this request </TH></TR>\n"); hPrintf("<TR><TH ALIGN=LEFT> SUMMARY: </TH>\n"); hPrintf("\t<TD> </TD>\n"); /* chromStart */ hPrintf("\t<TD> </TD>\n"); /* chromEnd */ hPrintf("\t<TD ALIGN=RIGHT> "); printLongWithCommas(stdout, statsItemCount); hPrintf(" </TD>\n" ); hPrintf("\t<TD ALIGN=RIGHT> %d </TD>\n", statsSpan); hPrintf("\t<TD ALIGN=RIGHT> "); printLongWithCommas(stdout, statsItemCount*statsSpan); hPrintf(" (%.2f%%) </TD>\n", 100.0*(double)(statsItemCount*statsSpan)/(double)realSize); hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", lowerLimit); hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit); hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit - lowerLimit); if (statsItemCount > 0) hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", statsSumData/statsItemCount); else hPrintf("\t<TD ALIGN=RIGHT> 0.0 </TD>\n"); stddev = 0.0; variance = 0.0; if (statsItemCount > 1) { variance = (statsSumSquares - ((statsSumData * statsSumData)/(double) statsItemCount)) / (double) (statsItemCount - 1); if (variance > 0.0) stddev = sqrt(variance); } hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", variance); hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", stddev); hPrintf("</TR>\n"); wigStatsTableHeading(stdout, TRUE); hPrintf("</TABLE></TD></TR></TABLE></P>\n"); } #if defined(NOT) /* can't do the histogram now, that operation times out */ /* Single region, we can do the histogram */ if ((valuesMatched > 1) && (1 == regionCount)) { float *valuesArray = NULL; size_t valueCount = 0; struct histoResult *histoGramResult; /* convert the ascii data listings to one giant float array */ valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount); /* histoGram() may return NULL if it doesn't work */ histoGramResult = histoGram(valuesArray, valueCount, NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit, (float) (wds->stats->lowerLimit + wds->stats->dataRange), (struct histoResult *)NULL); printHistoGram(histoGramResult, TRUE); /* TRUE == html output */ freeHistoGram(&histoGramResult); wds->freeAscii(wds); wds->freeArray(wds); } #endif wds->freeStats(wds); wiggleDataStreamFree(&wds); wigFetchTime = clock1000() - startTime; webNewSection("Region and Timing Statistics"); hTableStart(); stringStatRow("region", regionName); numberStatRow("bases in region", regionSize); numberStatRow("bases in gaps", gapTotal); floatStatRow("load and calc time", 0.001*wigFetchTime); wigFilterStatRow(conn); stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off")); hTableEnd(); htmlClose(); } /* void doSummaryStatsWiggle(struct sqlConnection *conn) */
static int wigOutRegion(char *table, struct sqlConnection *conn, struct region *region, int maxOut, enum wigOutputType wigOutType, struct wigAsciiData **data, int spanConstraint) /* Write out wig data in region. Write up to maxOut elements. * Returns number of elements written. */ { int linesOut = 0; char splitTableOrFileName[HDB_MAX_TABLE_STRING]; struct customTrack *ct = NULL; boolean isCustom = FALSE; boolean hasConstraint = FALSE; struct wiggleDataStream *wds = NULL; unsigned long long valuesMatched = 0; int operations = wigFetchAscii; char *dataConstraint; double ll = 0.0; double ul = 0.0; char *table2 = NULL; struct bed *intersectBedList = NULL; switch (wigOutType) { case wigOutBed: operations = wigFetchBed; break; default: case wigDataNoPrint: case wigOutData: operations = wigFetchAscii; break; }; WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */ if (hasConstraint) freeMem(dataConstraint); /* been cloned into wds */ wds->setMaxOutput(wds, maxOut); wds->setChromConstraint(wds, region->chrom); wds->setPositionConstraint(wds, region->start, region->end); if (table2) intersectBedList = bedTable2(conn, region, table2); if (isCustom) { if (ct->dbTrack) { if (spanConstraint) wds->setSpanConstraint(wds,spanConstraint); else { struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH); struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName); unsigned span = minSpan(trashConn, splitTableOrFileName, region->chrom, region->start, region->end, cart, tdb); wds->setSpanConstraint(wds, span); hFreeConn(&trashConn); } valuesMatched = getWigglePossibleIntersection(wds, region, CUSTOM_TRASH, table2, &intersectBedList, splitTableOrFileName, operations); } else valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2, &intersectBedList, splitTableOrFileName, operations); } else { if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL)) { /* XXX TBD, watch for a span limit coming in as an SQL filter */ if (intersectBedList) { struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName); unsigned span; span = minSpan(conn, splitTableOrFileName, region->chrom, region->start, region->end, cart, tdb); wds->setSpanConstraint(wds, span); } else if (spanConstraint) wds->setSpanConstraint(wds,spanConstraint); valuesMatched = getWigglePossibleIntersection(wds, region, database, table2, &intersectBedList, splitTableOrFileName, operations); } } switch (wigOutType) { case wigDataNoPrint: if (data) { if (*data != NULL) /* no exercise of this function yet */ { /* data not null, add to existing list */ struct wigAsciiData *asciiData; struct wigAsciiData *next; for (asciiData = *data; asciiData; asciiData = next) { next = asciiData->next; slAddHead(&wds->ascii, asciiData); } } wds->sortResults(wds); *data = wds->ascii; /* moving the list to *data */ wds->ascii = NULL; /* gone as far as wds is concerned */ } linesOut = valuesMatched; break; case wigOutBed: linesOut = wds->bedOut(wds, "stdout", TRUE);/* TRUE == sort output */ break; default: case wigOutData: linesOut = wds->asciiOut(wds, database, "stdout", TRUE, FALSE); break; /* TRUE == sort output, FALSE == not raw data out */ }; wiggleDataStreamFree(&wds); return linesOut; } /* static int wigOutRegion() */
struct bed *getWiggleAsBed( char *db, char *table, /* Database and table. */ struct region *region, /* Region to get data for. */ char *filter, /* Filter to add to SQL where clause if any. */ struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */ struct lm *lm, /* Where to allocate memory. */ struct sqlConnection *conn) /* SQL connection to work with */ /* Return a bed list of all items in the given range in table. * Cleanup result via lmCleanup(&lm) rather than bedFreeList. */ /* filter, idHash and lm are currently unused, perhaps future use */ { struct bed *bedList=NULL; char splitTableOrFileName[HDB_MAX_TABLE_STRING]; struct customTrack *ct = NULL; boolean isCustom = FALSE; boolean hasConstraint = FALSE; struct wiggleDataStream *wds = NULL; unsigned long long valuesMatched = 0; int operations = wigFetchBed; char *dataConstraint; double ll = 0.0; double ul = 0.0; char *table2 = NULL; struct bed *intersectBedList = NULL; int maxOut; WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */ if (hasConstraint) freeMem(dataConstraint); /* been cloned into wds */ maxOut = bigFileMaxOutput(); wds->setMaxOutput(wds, maxOut); wds->setChromConstraint(wds, region->chrom); wds->setPositionConstraint(wds, region->start, region->end); if (table2) intersectBedList = bedTable2(conn, region, table2); if (isCustom) { if (ct->dbTrack) { unsigned span = 0; struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH); struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName); valuesMatched = getWigglePossibleIntersection(wds, region, CUSTOM_TRASH, table2, &intersectBedList, splitTableOrFileName, operations); span = minSpan(trashConn, splitTableOrFileName, region->chrom, region->start, region->end, cart, tdb); wds->setSpanConstraint(wds, span); hFreeConn(&trashConn); } else valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2, &intersectBedList, splitTableOrFileName, operations); } else { if (conn == NULL) errAbort( "getWiggleAsBed: NULL conn given for database table"); if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL)) { struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName); unsigned span = 0; /* XXX TBD, watch for a span limit coming in as an SQL filter */ span = minSpan(conn, splitTableOrFileName, region->chrom, region->start, region->end, cart, tdb); wds->setSpanConstraint(wds, span); valuesMatched = getWigglePossibleIntersection(wds, region, database, table2, &intersectBedList, splitTableOrFileName, operations); } } if (valuesMatched > 0) { struct bed *bed; wds->sortResults(wds); for (bed = wds->bed; bed != NULL; bed = bed->next) { struct bed *copy = lmCloneBed(bed, lm); slAddHead(&bedList, copy); } slReverse(&bedList); } wiggleDataStreamFree(&wds); return bedList; } /* struct bed *getWiggleAsBed() */
void genericWiggleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display details for Wiggle data tracks. * conn may be NULL for custom tracks when from file */ { char *chrom = cartString(cart, "c"); char table[64]; boolean hasBin; unsigned span = 0; struct wiggleDataStream *wds = wiggleDataStreamNew(); unsigned long long valuesMatched = 0; struct histoResult *histoGramResult; float *valuesArray = NULL; size_t valueCount = 0; struct customTrack *ct = NULL; boolean isCustom = FALSE; int operations = wigFetchStats; /* default operation */ if (startsWith("ct_", tdb->table)) { ct = lookupCt(tdb->table); if (!ct) { warn("<P>wiggleClick: can not find custom wiggle track '%s'</P>", tdb->table); return; } if (! ct->wiggle) { warn("<P>wiggleClick: called to do stats on a custom track that isn't wiggle data ?</P>"); return; } if (ct->dbTrack) { safef(table,ArraySize(table), "%s", ct->dbTableName); span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb); } else { safef(table,ArraySize(table), "%s", ct->wigFile); span = 0; /* cause all spans to be examined */ } isCustom = TRUE; } else { hFindSplitTable(database, seqName, tdb->table, table, &hasBin); /*span = spanInUse(conn, table, chrom, winStart, winEnd, cart);*/ span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb); } /* if for some reason we don't have a chrom and win positions, this * should be run in a loop that does one chrom at a time. In the * case of hgc, there seems to be a chrom and a position. */ wds->setSpanConstraint(wds, span); wds->setChromConstraint(wds, chrom); wds->setPositionConstraint(wds, winStart, winEnd); /* If our window is less than some number of points, we can do * the histogram too. */ #define MAX_WINDOW_ALLOW_STATS 100000001 #define MAX_WINDOW_ALLOW_STRING "100,000,000" if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS) operations |= wigFetchAscii; /* We want to also fetch the actual data values so we can run a * histogram function on them. You can't fetch the data in the * form of the data array since the span information is then lost. * We have to do the ascii data list format, and prepare that to * send to the histogram function. */ if (isCustom) { if (ct->dbTrack) valuesMatched = wds->getData(wds, CUSTOM_TRASH, table, operations); else valuesMatched = wds->getData(wds, (char *)NULL, table, operations); } else valuesMatched = wds->getData(wds, database, table, operations); statsPreamble(wds, chrom, winStart, winEnd, span, valuesMatched, NULL); /* output statistics table * (+sort, +html output, +with header, +close table) */ wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE); if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS) { char *words[16]; int wordCount = 0; char *dupe = cloneString(tdb->type); double minY, maxY, tDbMinY, tDbMaxY; float hMin, hMax, hRange; wordCount = chopLine(dupe, words); wigFetchMinMaxY(tdb, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words); hMin = min(minY,tDbMinY); hMax = max(maxY,tDbMaxY); hRange = hMax - hMin; /* convert the ascii data listings to one giant float array */ valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount); /* let's see if we really want to use the range from the track type * line, or the actual range in this data. If there is a good * actual range in the data, use that instead */ if (hRange > 0.0) { if (wds->stats->dataRange != 0) hRange = 0.0; } /* If we have a valid range, use a specified 20 bin histogram * NOTE: pass 21 as binCount to get a 20 bin histogram */ if (hRange > 0.0) histoGramResult = histoGram(valuesArray, valueCount, (hRange/20.0), (unsigned) 21, hMin, hMin, hMax, (struct histoResult *)NULL); else histoGramResult = histoGram(valuesArray, valueCount, NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit, (float) (wds->stats->lowerLimit + wds->stats->dataRange), (struct histoResult *)NULL); /* histoGram() may return NULL if it doesn't work, that's OK, the * print out will indicate no results (TRUE == html output) */ printHistoGram(histoGramResult, TRUE); freeHistoGram(&histoGramResult); freeMem(valuesArray); } else { printf("<P>(viewing windows of fewer than %s bases will also" " display a histogram)</P>\n", MAX_WINDOW_ALLOW_STRING); } wiggleDataStreamFree(&wds); }