void printBiggestGap(char *database, struct sqlConnection *conn,
struct slName *chromList, struct hash *chromHash, char *track)
/* Look up track in database, figure out which type it is, call
* appropriate biggest gap finder, and then print result. */
{
struct trackDb *tdb = hTrackInfo(conn, track);
struct hTableInfo *hti = hFindTableInfo(database, chromList->name, tdb->table);
char *typeWord = cloneFirstWord(tdb->type);
boolean isBig = FALSE, isBigBed = FALSE;
struct bbiFile *bbi = NULL;
if (sameString(typeWord, "bigBed"))
{
isBig = TRUE;
isBigBed = TRUE;
bbi = bigBedFileOpen( bbiNameFromSettingOrTable(tdb, conn, tdb->table) );
}
else if (sameString(typeWord, "bigWig"))
{
isBig = TRUE;
bbi = bigWigFileOpen( bbiNameFromSettingOrTable(tdb, conn, tdb->table) );
}
char *biggestChrom = NULL;
int biggestSize = 0, biggestStart = 0, biggestEnd = 0;
struct slName *chrom;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
if (!allParts && strchr(chrom->name, '_')) // Generally skip weird chroms
continue;
if (female && sameString(chrom->name, "chrY"))
continue;
int chromSize = hashIntVal(chromHash, chrom->name);
struct rbTree *rt = rangeTreeNew();
int start = 0, end = 0, size = 0;
if (isBig)
bigCoverageIntoTree(tdb, bbi, chrom->name, chromSize, rt, isBigBed);
else
tableCoverageIntoTree(hti, tdb, conn, chrom->name, chromSize, rt);
if (rt->n > 0) // Want to keep completely uncovered chromosome uncovered
addGaps(conn, chrom->name, rt);
biggestGapFromRangeTree(rt, chromSize, &start, &end, &size);
if (size > biggestSize)
{
biggestSize = size;
biggestStart = start;
biggestEnd = end;
biggestChrom = chrom->name;
}
rangeTreeFree(&rt);
}
printf("%s\t%s:%d-%d\t", track, biggestChrom, biggestStart+1, biggestEnd);
if (noComma)
printf("%d", biggestSize);
else
printLongWithCommas(stdout, biggestSize);
putchar('\n');
freez(&typeWord);
bbiFileClose(&bbi);
}
void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
bigBedClick(fileName, tdb, item, start, end, bedSize);
}
struct bbiFile *fetchBbiForTrack(struct track *track)
/* Fetch bbiFile from track, opening it if it is not already open. */
{
struct bbiFile *bbi = track->bbiFile;
if (bbi == NULL)
{
char *fileName = NULL;
if (track->parallelLoading) // do not use mysql during parallel fetch
{
fileName = cloneString(trackDbSetting(track->tdb, "bigDataUrl"));
}
else
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConnTrack(database, track->tdb);
fileName = bbiNameFromSettingOrTable(track->tdb, conn, track->table);
hFreeConn(&conn);
}
#ifdef USE_GBIB_PWD
#include "gbib.c"
#endif
bbi = track->bbiFile = bigBedFileOpen(fileName);
}
return bbi;
}
static void bamWigLoadItems(struct track *tg)
{
char *fileName = NULL;
/* Figure out bigWig file name. */
if (tg->parallelLoading)
{
/* do not use mysql during parallel-fetch load */
fileName = trackDbSetting(tg->tdb, "bigDataUrl");
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
/* this should call bamFileNameFromTable with logic from bamLoadItemsCore to
* check the bigDataUrl setting. Fix this if bamWigs end up being
* a supported type. It may be that this code gets rolled into
* normal BAM display... since that's the plan ;-).
*/
fileName = bbiNameFromSettingOrTable(tg->tdb, conn, tg->table);
hFreeConn(&conn);
}
/* Allocate predraw area. */
struct bamWigTrackData *bwData;
double scale = (double)insideWidth/(winEnd - winStart);
struct preDrawContainer *pre = tg->preDrawContainer = initPreDrawContainer(insideWidth);
AllocVar(bwData);
bwData->preDraw = pre->preDraw;
bwData->scale = scale;
bwData->width = insideWidth;
bwData->preDrawZero = pre->preDrawZero;
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
bamFetch(fileName, posForBam, countBam, bwData, NULL);
/* fill in rest of predraw */
int preDrawZero = pre->preDrawZero;
int i;
for (i=0; i<insideWidth; ++i)
{
struct preDrawElement *pe = &bwData->preDraw[i + preDrawZero];
pe->min = pe->count;
pe->max = pe->count;
pe->sumData = pe->count / scale;
pe->sumSquares = (pe->count * pe->count)/scale;
}
}
static void vcfLoadItems(struct track *tg)
/* Load items in window from VCF file. */
{
int vcfMaxErr = -1;
struct vcfFile *vcff = NULL;
boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE);
char *table = tg->table;
struct customTrack *ct = tg->customPt;
struct sqlConnection *conn;
if (ct == NULL)
conn = hAllocConnTrack(database, tg->tdb);
else
{
conn = hAllocConn(CUSTOM_TRASH);
table = ct->dbTableName;
}
char *vcfFile = bbiNameFromSettingOrTable(tg->tdb, conn, table);
hFreeConn(&conn);
/* protect against parse error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
vcff = vcfFileMayOpen(vcfFile, chromName, winStart, winEnd, vcfMaxErr, -1, TRUE);
if (vcff != NULL)
{
filterRecords(vcff, tg->tdb);
if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 &&
(tg->visibility == tvPack || tg->visibility == tvSquish))
vcfHapClusterOverloadMethods(tg, vcff);
else
{
tg->items = vcfFileToPgSnp(vcff, tg->tdb);
// pgSnp bases coloring/display decision on count of items:
tg->customInt = slCount(tg->items);
}
// Don't vcfFileFree here -- we are using its string pointers!
}
}
errCatchEnd(errCatch);
if (errCatch->gotError || vcff == NULL)
{
if (isNotEmpty(errCatch->message->string))
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}