static unsigned long long getWigglePossibleIntersection(
struct wiggleDataStream *wds, struct region *region, char *db,
char *table2, struct bed **intersectBedList,
char splitTableOrFileName[256], int operations)
{
unsigned long long valuesMatched = 0;
/* Intersection is either type "any" or "none"
* The "none" case is already taken care of during the loading of
* table 2 since it was then inverted at that time so it is already
* "none" of itself.
*/
/* If table2 is NULL, it means that the WIG_INIT macro recognized that we
* are working on table2 now, so we should not use intersectBedList
* (in fact we may be trying to compute it here). */
if ((table2 != NULL) && anyIntersection())
{
if (*intersectBedList)
{
valuesMatched = wds->getDataViaBed(wds, db, splitTableOrFileName,
operations, intersectBedList);
}
}
else
{
valuesMatched = wds->getData(wds, db, splitTableOrFileName, operations);
}
return valuesMatched;
}
static void intersectDataVector(char *table, struct dataVector *dataVector1,
struct region *region, struct sqlConnection *conn)
/* Perform intersection (if specified) on dataVector. */
{
/* If table is type wig (not bedGraph), then intersection has already been
* performed on each input (other selected subtracks must be the same type
* as table).
* Otherwise, handle intersection here. */
if (anyIntersection() && !isWiggle(database, table) && !isBigWigTable(table))
{
char *track2 = cartString(cart, hgtaIntersectTrack);
char *table2 = cartString(cart, hgtaIntersectTable);
if (table2 && differentWord(table2, table))
{
struct trackDb *tdb2 = findTrack(track2, fullTrackList);
struct trackTable *tt2 = trackTableNew(tdb2, table2, conn);
struct dataVector *dataVector2 = dataVectorFetchOneRegion(tt2, region,
conn);
char *op = cartString(cart, hgtaIntersectOp);
boolean dv2IsWiggle = (isWiggle(database, table2) || isBigWigTable(table2) ||
isBedGraph(table2));
dataVectorIntersect(dataVector1, dataVector2,
dv2IsWiggle, sameString(op, "none"));
dataVectorFree(&dataVector2);
}
}
}
void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
static struct bed *getIntersectedBeds(struct sqlConnection *conn,
char *table, struct region *region, struct lm *lm, int *retFieldCount)
/* Get list of beds in region that pass intersection
* (and filtering) */
{
struct bed *bedList = getFilteredBeds(conn, table, region, lm, retFieldCount);
/* wiggle tracks have already done the intersection if there was one */
if (!isWiggle(database, table) && anyIntersection())
{
struct bed *iBedList = intersectOnRegion(conn, region, table, bedList,
lm, retFieldCount);
return iBedList;
}
else
return bedList;
}
int bigWigOutRegion(char *table, struct sqlConnection *conn,
struct region *region, int maxOut,
enum wigOutputType wigOutType)
/* Write out bigWig for region, doing intersecting and filtering as need be. */
{
boolean isMerged = anySubtrackMerge(table, database);
int resultCount = 0;
char *wigFileName = bigWigFileName(table, conn);
if (wigFileName)
{
struct bbiFile *bwf = bigWigFileOpen(wigFileName);
if (bwf)
{
/* Easy case, just dump out data. */
if (!anyFilter() && !anyIntersection() && !isMerged && wigOutType == wigOutData)
resultCount = bigWigIntervalDump(bwf, region->chrom, region->start, region->end,
maxOut, stdout);
/* Pretty easy case, still do it ourselves. */
else if (!isMerged && wigOutType == wigOutData)
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
struct lm *lm = lmInit(0);
struct bbiInterval *ivList, *iv;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv=ivList; iv != NULL && resultCount < maxOut; iv = iv->next, ++resultCount)
{
fprintf(stdout, "%s\t%d\t%d\t%g\n", region->chrom, iv->start, iv->end, iv->val);
}
lmCleanup(&lm);
}
/* Harder cases - resort to making a data vector and letting that machinery handle it. */
else
{
struct dataVector *dv = bigWigDataVector(table, conn, region);
resultCount = wigPrintDataVectorOut(dv, wigOutType, maxOut, NULL);
dataVectorFree(&dv);
}
}
bbiFileClose(&bwf);
}
freeMem(wigFileName);
return resultCount;
}
void doOutSelectedFields(char *table, struct sqlConnection *conn)
/* Put up select fields (for tab-separated output) page. */
{
if (anySubtrackMerge(database, curTable))
errAbort("Can't do selected fields output when subtrack merge is on. "
"Please go back and select another output type, or clear the subtrack merge.");
else if (anyIntersection())
errAbort("Can't do selected fields output when intersection is on. "
"Please go back and select another output type, or clear the intersection.");
else
{
char *fsTable = cartOptionalString(cart, hgtaFieldSelectTable);
char *dbTable = NULL;
table = connectingTableForTrack(table);
dbTable = getDbTable(database, table);
/* Remove cart state if table has been changed: */
if (fsTable && ! sameString(fsTable, dbTable))
{
cartRemovePrefix(cart, hgtaFieldSelectPrefix);
cartRemove(cart, hgtaFieldSelectTable);
}
doBigSelectPage(database, table);
}
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
void doSummaryStatsBed(struct sqlConnection *conn)
/* Put up page showing summary stats for track that is in database
* or that is bed-format custom. */
{
struct bed *bedList = NULL;
struct region *regionList = getRegions(), *region;
char *regionName = getRegionName();
long long regionSize = 0, gapTotal = 0, realSize = 0;
long startTime, midTime, endTime;
long loadTime = 0, calcTime = 0, freeTime = 0;
struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov;
int itemCount = 0;
struct hTableInfo *hti = getHti(database, curTable, conn);
int minScore = BIGNUM, maxScore = -BIGNUM;
long long sumScores = 0;
boolean hasBlocks = hti->hasBlocks;
boolean hasScore = (hti->scoreField[0] != 0);
int fieldCount;
htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
startTime = clock1000();
bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
if (fieldCount < 12)
hasBlocks = FALSE;
if (fieldCount < 5)
hasScore = FALSE;
midTime = clock1000();
loadTime += midTime - startTime;
if (bedList != NULL)
{
itemCount += slCount(bedList);
regionSize += region->end - region->start;
cov = calcSpanOverRegion(region, bedList);
slAddHead(&itemCovList, cov);
if (hasBlocks)
{
cov = calcBlocksOverRegion(region, bedList);
slAddHead(&blockCovList, cov);
}
if (hti->scoreField[0] != 0)
{
struct bed *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
int score = bed->score;
if (score < minScore) minScore = score;
if (score > maxScore) maxScore = score;
sumScores += score;
}
}
}
endTime = clock1000();
calcTime += endTime - midTime;
lmCleanup(&lm);
bedList = NULL;
freeTime += clock1000() - endTime;
}
regionSize = basesInRegion(regionList, 0);
gapTotal = gapsInRegion(conn, regionList, 0);
realSize = regionSize - gapTotal;
hTableStart();
startTime = clock1000();
numberStatRow("item count", itemCount);
if (itemCount > 0)
{
cov = covStatsSum(itemCovList);
percentStatRow("item bases", cov->basesCovered, realSize);
percentStatRow("item total", cov->sumBases, realSize);
numberStatRow("smallest item", cov->minBases);
numberStatRow("average item", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest item", cov->maxBases);
}
if (hasBlocks && itemCount > 0)
{
cov = covStatsSum(blockCovList);
hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>");
printLongWithCommas(stdout, cov->itemCount);
hPrintf("</TD></TR>\n");
percentStatRow("block bases", cov->basesCovered, realSize);
percentStatRow("block total", cov->sumBases, realSize);
numberStatRow("smallest block", cov->minBases);
numberStatRow("average block", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest block", cov->maxBases);
}
if (hasScore != 0 && itemCount > 0 && sumScores != 0)
{
numberStatRow("smallest score", minScore);
numberStatRow("average score", round((double)sumScores/itemCount));
numberStatRow("biggest score", maxScore);
}
hTableEnd();
/* Show region and time stats part of stats page. */
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load time", 0.001*loadTime);
floatStatRow("calculation time", 0.001*calcTime);
floatStatRow("free memory time", 0.001*freeTime);
stringStatRow("filter", (anyFilter() ? "on" : "off"));
stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
hTableEnd();
covStatsFreeList(&itemCovList);
covStatsFreeList(&blockCovList);
htmlClose();
}
void showMainControlTable(struct sqlConnection *conn)
/* Put up table with main controls for main page. */
{
struct grp *selGroup;
boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;
hPrintf("<TABLE BORDER=0>\n");
/* Print clade, genome and assembly line. */
{
if (gotClade)
{
hPrintf("<TR><TD><B>clade:</B>\n");
printCladeListHtml(hGenome(database), onChangeClade());
nbSpaces(3);
hPrintf("<B>genome:</B>\n");
printGenomeListForCladeHtml(database, onChangeOrg());
}
else
{
hPrintf("<TR><TD><B>genome:</B>\n");
printGenomeListHtml(database, onChangeOrg());
}
nbSpaces(3);
hPrintf("<B>assembly:</B>\n");
printAssemblyListHtml(database, onChangeDb());
hPrintf("</TD></TR>\n");
}
/* Print group and track line. */
{
hPrintf("<TR><TD>");
selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
nbSpaces(3);
curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
nbSpaces(3);
boolean hasCustomTracks = FALSE;
struct trackDb *t;
for (t = fullTrackList; t != NULL; t = t->next)
{
if (isCustomTrack(t->table))
{
hasCustomTracks = TRUE;
break;
}
}
hOnClickButton("document.customTrackForm.submit();return false;",
hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
hPrintf(" ");
if (hubConnectTableExists())
hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
hPrintf("</TD></TR>\n");
}
/* Print table line. */
{
hPrintf("<TR><TD>");
curTable = showTableField(curTrack, hgtaTable, TRUE);
if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL)) /* In same database */
{
hti = getHti(database, curTable, conn);
isPositional = htiIsPositional(hti);
}
isLongTabix = isLongTabixTable( curTable);
isBam = isBamTable( curTable);
isVcf = isVcfTable(curTable, NULL);
isWig = isWiggle(database, curTable);
if (isBigWigTable(curTable))
{
isPositional = TRUE;
isWig = TRUE;
}
isHalSnake = isHalTable( curTable);
isMaf = isMafTable(database, curTrack, curTable);
isBedGr = isBedGraph(curTable);
isArray = isMicroarray(curTrack, curTable);
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
isPal = isPalCompatible(conn, tdb, curTable);
nbSpaces(1);
if (isCustomTrack(curTable))
{
isChromGraphCt = isChromGraph(tdb);
}
cgiMakeButton(hgtaDoSchema, "describe table schema");
hPrintf("</TD></TR>\n");
}
if (curTrack == NULL)
{
struct trackDb *tdb = hTrackDbForTrack(database, curTable);
struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
if (cTdb)
curTrack = cTdb;
else
curTrack = tdb;
isMaf = isMafTable(database, curTrack, curTable);
}
/* Region line */
{
char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
{
boolean doEncode = FALSE;
if (!trackHubDatabase(database))
doEncode = sqlTableExists(conn, "encodeRegions");
hPrintf("<TR><TD><B>region:</B>\n");
/* If regionType not allowed force it to "genome". */
if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
userRegionsFileName() == NULL) ||
(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
regionType = hgtaRegionTypeGenome;
// Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
(curTable && cartTrackDbIsNoGenome(database, curTable)));
// If "genome" is selected but not allowed, force it to "range":
if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
regionType = hgtaRegionTypeRange;
jsTrackingVar("regionType", regionType);
if (disableGenome)
{
makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
hPrintf(" <span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
" ");
}
else
{
makeRegionButton(hgtaRegionTypeGenome, regionType);
hPrintf(" genome ");
}
if (doEncode)
{
makeRegionButton(hgtaRegionTypeEncode, regionType);
hPrintf(" ENCODE Pilot regions ");
}
makeRegionButton(hgtaRegionTypeRange, regionType);
hPrintf(" position ");
hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
cgiMakeButton(hgtaDoLookupPosition, "lookup");
hPrintf(" ");
if (userRegionsFileName() != NULL)
{
makeRegionButton(hgtaRegionTypeUserRegions, regionType);
hPrintf(" defined regions ");
cgiMakeButton(hgtaDoSetUserRegions, "change");
hPrintf(" ");
cgiMakeButton(hgtaDoClearUserRegions, "clear");
}
else
cgiMakeButton(hgtaDoSetUserRegions, "define regions");
hPrintf("</TD></TR>\n");
}
else
{
/* Need to put at least stubs of cgi variables in for JavaScript to work. */
jsTrackingVar("regionType", regionType);
cgiMakeHiddenVar(hgtaRange, range);
cgiMakeHiddenVar(hgtaRegionType, regionType);
}
/* Select identifiers line (if applicable). */
if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
{
hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
hPrintf(" ");
cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
if (identifierFileName() != NULL)
{
hPrintf(" ");
cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
}
hPrintf("</TD></TR>\n");
}
}
/* microarray options */
/* button for option page here (median/log-ratio, etc) */
/* Filter line. */
{
hPrintf("<TR><TD><B>filter:</B>\n");
if (anyFilter())
{
cgiMakeButton(hgtaDoFilterPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearFilter, "clear");
if (isWig || isBedGr)
wigShowFilter(conn);
}
else
{
cgiMakeButton(hgtaDoFilterPage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix);
if (canSubtrackMerge)
{
hPrintf("<TR><TD><B>subtrack merge:</B>\n");
if (anySubtrackMerge(database, curTable))
{
cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
}
else
{
cgiMakeButton(hgtaDoSubtrackMergePage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Intersection line. */
if (isPositional)
{
if (anyIntersection())
{
hPrintf("<TR><TD><B>intersection with %s:</B>\n",
cartString(cart, hgtaIntersectTable));
cgiMakeButton(hgtaDoIntersectPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearIntersect, "clear");
hPrintf("</TD></TR>\n");
}
else if (canIntersect(database, curTable))
{
hPrintf("<TR><TD><B>intersection:</B>\n");
cgiMakeButton(hgtaDoIntersectPage, "create");
hPrintf("</TD></TR>\n");
}
}
/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
{
char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
hPrintf("<TR><TD><B>correlation:</B>\n");
if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2))
{
struct grp *groupList = fullGroupList;
struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
if (tdbIsComposite(tdb2))
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
if (sameString(table2, subTdb->table))
{
tdb2 = subTdb;
break;
}
}
slFreeList(&tdbRefList);
}
cgiMakeButton(hgtaDoCorrelatePage, "calculate");
cgiMakeButton(hgtaDoClearCorrelate, "clear");
if (tdb2 && tdb2->shortLabel)
hPrintf(" (with: %s)", tdb2->shortLabel);
#ifdef NOT_YET
/* debugging dbg vvvvv */
if (curTrack && curTrack->type) /* dbg */
{
hPrintf("<BR> (debug: '%s', '%s(%s)')",
curTrack->type, tdb2->type, table2);
}
/* debugging debug ^^^^^ */
#endif
}
else
cgiMakeButton(hgtaDoCorrelatePage, "create");
hPrintf("</TD></TR>\n");
}
/* Print output type line. */
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
/* Print output destination line. */
{
char *compressType =
cartUsualString(cart, hgtaCompressType, textOutCompressNone);
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
hPrintf("<TR><TD>\n");
hPrintf("<B>output file:</B> ");
cgiMakeTextVar(hgtaOutFileName, fileName, 29);
hPrintf(" (leave blank to keep output in browser)</TD></TR>\n");
hPrintf("<TR><TD>\n");
hPrintf("<B>file type returned: </B>");
cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
sameWord(textOutCompressNone, compressType));
hPrintf(" plain text  ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
sameWord(textOutCompressGzip, compressType));
hPrintf(" gzip compressed");
hPrintf("</TD></TR>\n");
}
hPrintf("</TABLE>\n");
/* Submit buttons. */
{
hPrintf("<BR>\n");
if (isWig || isBam || isVcf || isLongTabix)
{
char *name;
extern char *maxOutMenu[];
char *maxOutput = maxOutMenu[0];
if (isCustomTrack(curTable))
name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
else
name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);
maxOutput = cartUsualString(cart, name, maxOutMenu[0]);
if (isWig)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). The entire data set may be available for download as"
" a very large file that contains the original data values (not"
" compressed into the wiggle format) -- see the Downloads page."
"</I><BR>", maxOutput);
else if (isBam || isVcf || isLongTabix)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). Please consider downloading the entire data from our Download pages."
"</I><BR>", maxOutput);
}
else if (anySubtrackMerge(database, curTable) || anyIntersection())
{
hPrintf("<I>Note: The all fields and selected fields output formats "
"are not available when a%s has been specified.</I><BR>",
canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
}
cgiMakeButton(hgtaDoTopSubmit, "get output");
hPrintf(" ");
if (isPositional || isWig)
{
cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
hPrintf(" ");
}
#ifdef SOMETIMES
hPrintf(" ");
cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
}
hPrintf("<P>"
"To reset <B>all</B> user cart settings (including custom tracks), \n"
"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
getScriptName());
}
static void showOutputTypeRow(boolean isWig, boolean isBedGr,
boolean isPositional, boolean isMaf, boolean isChromGraphCt,
boolean isPal, boolean isMicroarray, boolean isHalSnake)
/* Print output line. */
{
struct outputType *otList = NULL, *otDefault = NULL;
boolean bedifiedOnly = (anySubtrackMerge(database, curTable) || anyIntersection());
hPrintf("<TR><TD><B>output format:</B>\n");
if (isBedGr)
{
if (! bedifiedOnly)
{
slAddTail(&otList, &otAllFields);
slAddTail(&otList, &otSelected);
}
slAddTail(&otList, &otWigData);
slAddTail(&otList, &otWigBed);
slAddTail(&otList, &otCustomTrack);
slAddTail(&otList, &otHyperlinks);
}
else if (isWig)
{
slAddTail(&otList, &otWigData);
slAddTail(&otList, &otWigBed);
slAddTail(&otList, &otCustomTrack);
// hyperlinks output works for db-wiggle but not for bigWig
}
else if (isHalSnake)
{
slAddTail(&otList, &otMaf);
}
else if (isMaf)
{
slAddTail(&otList, &otMaf);
if (! bedifiedOnly)
slAddTail(&otList, &otAllFields);
}
else if (isChromGraphCt)
{
slAddTail(&otList, &otChromGraphData);
}
else if (isMicroarray)
{
slAddTail(&otList, &otMicroarrayNames);
slAddTail(&otList, &otAllFields);
slAddTail(&otList, &otSelected);
slAddTail(&otList, &otHyperlinks);
}
else if (isPositional)
{
if (! bedifiedOnly)
{
slAddTail(&otList, &otAllFields);
slAddTail(&otList, &otSelected);
}
else
otDefault = &otBed;
slAddTail(&otList, &otSequence);
slAddTail(&otList, &otGff);
if (isPal)
slAddTail(&otList, &otPal);
slAddTail(&otList, &otBed);
slAddTail(&otList, &otCustomTrack);
slAddTail(&otList, &otHyperlinks);
}
else
{
slAddTail(&otList, &otAllFields);
slAddTail(&otList, &otSelected);
}
showOutDropDown(otList, otDefault);
}
struct bbiInterval *intersectedFilteredBbiIntervalsOnRegion(struct sqlConnection *conn,
struct bbiFile *bwf, struct region *region, enum wigCompare filterCmp, double filterLl,
double filterUl, struct lm *lm)
/* Get list of bbiIntervals (more-or-less bedGraph things from bigWig) out of bigWig file
* and if necessary apply filter and intersection. Return list which is allocated in lm. */
{
char *chrom = region->chrom;
int chromSize = hChromSize(database, chrom);
struct bbiInterval *iv, *ivList = bigWigIntervalQuery(bwf, chrom, region->start, region->end, lm);
/* Run filter if necessary */
if (filterCmp != wigNoOp_e)
{
struct bbiInterval *next, *newList = NULL;
for (iv = ivList; iv != NULL; iv = next)
{
next = iv->next;
if (wigCompareValFilter(iv->val, filterCmp, filterLl, filterUl))
{
slAddHead(&newList, iv);
}
}
slReverse(&newList);
ivList = newList;
}
/* Run intersection if necessary */
if (anyIntersection())
{
boolean isBpWise = intersectionIsBpWise();
Bits *bits2 = bitsForIntersectingTable(conn, region, chromSize, isBpWise);
struct bbiInterval *next, *newList = NULL;
double moreThresh = cartCgiUsualDouble(cart, hgtaMoreThreshold, 0)*0.01;
double lessThresh = cartCgiUsualDouble(cart, hgtaLessThreshold, 100)*0.01;
char *op = cartString(cart, hgtaIntersectOp);
for (iv = ivList; iv != NULL; iv = next)
{
next = iv->next;
int start = iv->start;
int size = iv->end - start;
int overlap = bitCountRange(bits2, start, size);
if (isBpWise)
{
if (overlap == size)
{
slAddHead(&newList, iv);
}
else if (overlap > 0)
{
/* Here we have to break things up. */
double val = iv->val;
struct bbiInterval *partIv = iv; // Reuse memory for first interval
int s = iv->start, end = iv->end;
for (;;)
{
s = bitFindSet(bits2, s, end);
if (s >= end)
break;
int bitsSet = bitFindClear(bits2, s, end) - s;
if (partIv == NULL)
lmAllocVar(lm, partIv);
partIv->start = s;
partIv->end = s + bitsSet;
partIv->val = val;
slAddHead(&newList, partIv);
partIv = NULL;
s += bitsSet;
if (s >= end)
break;
}
}
}
else
{
double coverage = (double)overlap/size;
if (intersectOverlapFilter(op, moreThresh, lessThresh, coverage))
{
slAddHead(&newList, iv);
}
}
}
slReverse(&newList);
ivList = newList;
bitFree(&bits2);
}
return ivList;
}
void doSummaryStatsBigWig(struct sqlConnection *conn)
/* Put up page showing summary stats for bigWig track. */
{
struct trackDb *track = curTrack;
char *table = curTable;
char *shortLabel = (track == NULL ? table : track->shortLabel);
char *fileName = bigWigFileName(table, conn);
long startTime = clock1000();
htmlOpen("%s (%s) Big Wig 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);
struct bbiFile *bwf = bigWigFileOpen(fileName);
struct region *region, *regionList = getRegions();
double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
bits64 validCount = 0;
if (!anyFilter() && !anyIntersection())
{
for (region = regionList; region != NULL; region = region->next)
{
struct bbiSummaryElement sum;
if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
bigWigIntervalQuery, 1, &sum))
{
if (validCount == 0)
{
minVal = sum.minVal;
maxVal = sum.maxVal;
}
else
{
if (sum.minVal < minVal)
minVal = sum.minVal;
if (sum.maxVal > maxVal)
maxVal = sum.maxVal;
}
sumData += sum.sumData;
sumSquares += sum.sumSquares;
validCount += sum.validCount;
}
}
}
else
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(0);
struct bbiInterval *iv, *ivList;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
double size = iv->end - iv->start;
if (validCount == 0)
minVal = maxVal = val;
else
{
if (val < minVal)
minVal = val;
if (val > maxVal)
maxVal = val;
}
sumData += size*val;
sumSquares += size*val*val;
validCount += size;
}
lmCleanup(&lm);
}
}
hTableStart();
floatStatRow("mean", sumData/validCount);
floatStatRow("min", minVal);
floatStatRow("max", maxVal);
floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
numberStatRow("bases with data", validCount);
long long regionSize = basesInRegion(regionList,0);
long long gapTotal = gapsInRegion(conn, regionList,0);
numberStatRow("bases with sequence", regionSize - gapTotal);
numberStatRow("bases in region", regionSize);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
long wigFetchTime = clock1000() - startTime;
floatStatRow("load and calc time", 0.001*wigFetchTime);
hTableEnd();
bbiFileClose(&bwf);
htmlClose();
}
