void printEnrichment(struct sqlConnection *conn, long long fileId, char *target, FILE *f)
/* Get enrichment for file and target and print it if possible. */
{
struct edwQaEnrich *enrich = edwQaEnrichFind(conn, fileId, target);
if (enrich != NULL)
{
fprintf(f, "<TD>%4.2fx</TD>\n", enrich->enrichment);
fprintf(f, "<TD>%4.3f</TD>\n", enrich->coverage);
}
else
{
fprintf(f, "<TD>n/a</TD>\n");
fprintf(f, "<TD>n/a</TD>\n");
}
edwQaEnrichFree(&enrich);
}
void doEnrichmentsFromSampleBed(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf,
struct edwAssembly *assembly, struct target *targetList)
/* Figure out enrichments from sample bed file. */
{
char *sampleBed = vf->sampleBed;
if (isEmpty(sampleBed))
{
warn("No sample bed for %s", ef->edwFileName);
return;
}
/* Load sample bed, make a range tree to track unique coverage, and get list of all chroms .*/
struct bed3 *sample, *sampleList = bed3LoadAll(sampleBed);
if (sampleList == NULL)
{
warn("Sample bed is empty for %s", ef->edwFileName);
return;
}
struct genomeRangeTree *sampleGrt = edwMakeGrtFromBed3List(sampleList);
struct hashEl *chrom, *chromList = hashElListHash(sampleGrt->hash);
/* Iterate through each target - and in lockstep each associated grt to calculate unique overlap */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct genomeRangeTree *grt = target->grt;
long long uniqOverlapBases = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct rbTree *sampleTree = chrom->val;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
struct range *range, *rangeList = rangeTreeList(sampleTree);
for (range = rangeList; range != NULL; range = range->next)
{
/* Do unique base overlap counts (since using range trees both sides) */
int overlap = rangeTreeOverlapSize(targetTree, range->start, range->end);
uniqOverlapBases += overlap;
}
}
}
/* Figure out how much we overlap allowing same bases in genome
* to part of more than one overlap. */
long long overlapBases = 0;
for (sample = sampleList; sample != NULL; sample = sample->next)
{
int overlap = genomeRangeTreeOverlapSize(grt,
sample->chrom, sample->chromStart, sample->chromEnd);
overlapBases += overlap;
}
/* Save to database. */
struct edwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly,
target, overlapBases, uniqOverlapBases);
edwQaEnrichSaveToDb(conn, enrich, "edwQaEnrich", 128);
edwQaEnrichFree(&enrich);
}
genomeRangeTreeFree(&sampleGrt);
bed3FreeList(&sampleList);
hashElFreeList(&chromList);
}
/* This old way is ~3 times as slow */
void doEnrichmentsFromBigWig(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf,
struct edwAssembly *assembly, struct target *targetList)
/* Figure out enrichments from a bigBed file. */
{
/* Get path to bigBed, open it, and read all chromosomes. */
char *bigWigPath = edwPathForFileId(conn, ef->id);
struct bbiFile *bbi = bigWigFileOpen(bigWigPath);
struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
/* This takes a while, so let's figure out what parts take the time. */
long totalBigQueryTime = 0;
long totalOverlapTime = 0;
/* Do a pretty complex loop that just aims to set target->overlapBases and ->uniqOverlapBases
* for all targets. This is complicated by just wanting to keep one chromosome worth of
* bigWig data in memory. Also just for performance we do a lookup of target range tree to
* get chromosome specific one to use, which avoids a hash lookup in the inner loop. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
/* Get list of intervals in bigWig for this chromosome, and feed it to a rangeTree. */
struct lm *lm = lmInit(0);
long startBigQueryTime = clock1000();
struct bbiInterval *ivList = bigWigIntervalQuery(bbi, chrom->name, 0, chrom->size, lm);
long endBigQueryTime = clock1000();
totalBigQueryTime += endBigQueryTime - startBigQueryTime;
struct bbiInterval *iv;
/* Loop through all targets adding overlaps from ivList */
long startOverlapTime = clock1000();
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
struct genomeRangeTree *grt = target->grt;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
for (iv = ivList; iv != NULL; iv = iv->next)
{
int overlap = rangeTreeOverlapSize(targetTree, iv->start, iv->end);
target->uniqOverlapBases += overlap;
target->overlapBases += overlap * iv->val;
}
}
}
long endOverlapTime = clock1000();
totalOverlapTime += endOverlapTime - startOverlapTime;
lmCleanup(&lm);
}
verbose(1, "totalBig %0.3f, totalOverlap %0.3f\n", 0.001*totalBigQueryTime, 0.001*totalOverlapTime);
/* Now loop through targets and save enrichment info to database */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
struct edwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly, target,
target->overlapBases, target->uniqOverlapBases);
edwQaEnrichSaveToDb(conn, enrich, "edwQaEnrich", 128);
edwQaEnrichFree(&enrich);
}
bbiChromInfoFreeList(&chromList);
bigWigFileClose(&bbi);
freez(&bigWigPath);
}
void doEnrichmentsFromBigWig(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf,
struct edwAssembly *assembly, struct target *targetList)
/* Figure out enrichments from a bigBed file. */
{
/* Get path to bigBed, open it, and read all chromosomes. */
char *bigWigPath = edwPathForFileId(conn, ef->id);
struct bbiFile *bbi = bigWigFileOpen(bigWigPath);
struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
struct bigWigValsOnChrom *valsOnChrom = bigWigValsOnChromNew();
/* This takes a while, so let's figure out what parts take the time. */
long totalBigQueryTime = 0;
long totalOverlapTime = 0;
/* Do a pretty complex loop that just aims to set target->overlapBases and ->uniqOverlapBases
* for all targets. This is complicated by just wanting to keep one chromosome worth of
* bigWig data in memory. Also just for performance we do a lookup of target range tree to
* get chromosome specific one to use, which avoids a hash lookup in the inner loop. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
long startBigQueryTime = clock1000();
boolean gotData = bigWigValsOnChromFetchData(valsOnChrom, chrom->name, bbi);
long endBigQueryTime = clock1000();
totalBigQueryTime += endBigQueryTime - startBigQueryTime;
if (gotData)
{
double *valBuf = valsOnChrom->valBuf;
Bits *covBuf = valsOnChrom->covBuf;
/* Loop through all targets adding overlaps from ivList */
long startOverlapTime = clock1000();
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct genomeRangeTree *grt = target->grt;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
struct range *range, *rangeList = rangeTreeList(targetTree);
for (range = rangeList; range != NULL; range = range->next)
{
int s = range->start, e = range->end, i;
for (i=s; i<=e; ++i)
{
if (bitReadOne(covBuf, i))
{
double x = valBuf[i];
target->uniqOverlapBases += 1;
target->overlapBases += x;
}
}
}
}
}
long endOverlapTime = clock1000();
totalOverlapTime += endOverlapTime - startOverlapTime;
}
}
verbose(1, "totalBig %0.3f, totalOverlap %0.3f\n", 0.001*totalBigQueryTime, 0.001*totalOverlapTime);
/* Now loop through targets and save enrichment info to database */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct edwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly, target,
target->overlapBases, target->uniqOverlapBases);
edwQaEnrichSaveToDb(conn, enrich, "edwQaEnrich", 128);
edwQaEnrichFree(&enrich);
}
bigWigValsOnChromFree(&valsOnChrom);
bbiChromInfoFreeList(&chromList);
bigWigFileClose(&bbi);
freez(&bigWigPath);
}
void doEnrichmentsFromBigBed(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf,
struct edwAssembly *assembly, struct target *targetList)
/* Figure out enrichments from a bigBed file. */
{
/* Get path to bigBed, open it, and read all chromosomes. */
char *bigBedPath = edwPathForFileId(conn, ef->id);
struct bbiFile *bbi = bigBedFileOpen(bigBedPath);
struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
/* Do a pretty complex loop that just aims to set target->overlapBases and ->uniqOverlapBases
* for all targets. This is complicated by just wanting to keep one chromosome worth of
* bigBed data in memory. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
/* Get list of intervals in bigBed for this chromosome, and feed it to a rangeTree. */
struct lm *lm = lmInit(0);
struct bigBedInterval *ivList = bigBedIntervalQuery(bbi, chrom->name, 0, chrom->size, 0, lm);
struct bigBedInterval *iv;
struct rbTree *bbTree = rangeTreeNew();
for (iv = ivList; iv != NULL; iv = iv->next)
rangeTreeAdd(bbTree, iv->start, iv->end);
struct range *bbRange, *bbRangeList = rangeTreeList(bbTree);
/* Loop through all targets adding overlaps from ivList and unique overlaps from bbRangeList */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct genomeRangeTree *grt = target->grt;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
struct bigBedInterval *iv;
for (iv = ivList; iv != NULL; iv = iv->next)
{
int overlap = rangeTreeOverlapSize(targetTree, iv->start, iv->end);
target->overlapBases += overlap;
}
for (bbRange = bbRangeList; bbRange != NULL; bbRange = bbRange->next)
{
int overlap = rangeTreeOverlapSize(targetTree, bbRange->start, bbRange->end);
target->uniqOverlapBases += overlap;
}
}
}
rangeTreeFree(&bbTree);
lmCleanup(&lm);
}
/* Now loop through targets and save enrichment info to database */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct edwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly, target,
target->overlapBases, target->uniqOverlapBases);
edwQaEnrichSaveToDb(conn, enrich, "edwQaEnrich", 128);
edwQaEnrichFree(&enrich);
}
bbiChromInfoFreeList(&chromList);
bigBedFileClose(&bbi);
freez(&bigBedPath);
}
