void doBed3Replicate(struct sqlConnection *conn, char *format, struct cdwAssembly *assembly,
struct cdwFile *elderEf, struct cdwValidFile *elderVf, struct bed3 *elderBedList,
struct cdwFile *youngerEf, struct cdwValidFile *youngerVf, struct bed3 *youngerBedList)
/* Do correlation analysis between elder and younger bedLists and save result to
* a new cdwQaPairSampleOverlap record. Do this for a format where we have a bed3 sample file. */
{
struct cdwQaPairSampleOverlap *sam;
AllocVar(sam);
sam->elderFileId = elderVf->fileId;
sam->youngerFileId = youngerVf->fileId;
sam->elderSampleBases = elderVf->basesInSample;
sam->youngerSampleBases = youngerVf->basesInSample;
/* Load up elder into genome range tree. */
struct genomeRangeTree *elderGrt = cdwMakeGrtFromBed3List(elderBedList);
/* Load up younger as bed, and loop through to get overlap */
long long totalOverlap = 0;
struct bed3 *bed;
for (bed = youngerBedList; bed != NULL; bed = bed->next)
{
int overlap = genomeRangeTreeOverlapSize(elderGrt,
bed->chrom, bed->chromStart, bed->chromEnd);
totalOverlap += overlap;
}
sam->sampleOverlapBases = totalOverlap;
setSampleSampleEnrichment(sam, format, assembly, elderVf, youngerVf);
/* Save to database, clean up, go home. */
cdwQaPairSampleOverlapSaveToDb(conn, sam, "cdwQaPairSampleOverlap", 128);
freez(&sam);
genomeRangeTreeFree(&elderGrt);
}
long getAnnotatedNonGapBases(struct genomeRangeTree* ranges, struct bed* antigaps)
{
long retval = 0;
struct bed* currAntigap;
for (currAntigap = antigaps; currAntigap != NULL; currAntigap = currAntigap->next) {
retval += genomeRangeTreeOverlapSize(ranges, currAntigap->chrom, currAntigap->chromStart, currAntigap->chromEnd);
}
return retval;
}
void doEnrichmentsFromBed3Sample(struct bed3 *sampleList,
struct sqlConnection *conn,
struct cdwFile *ef, struct cdwValidFile *vf,
struct cdwAssembly *assembly, struct target *targetList)
/* Given a bed3 list, calculate enrichments for targets */
{
struct genomeRangeTree *sampleGrt = cdwMakeGrtFromBed3List(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;
struct bed3 *sample;
for (sample = sampleList; sample != NULL; sample = sample->next)
{
int overlap = genomeRangeTreeOverlapSize(grt,
sample->chrom, sample->chromStart, sample->chromEnd);
overlapBases += overlap;
}
/* Save to database. */
struct cdwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly,
target, overlapBases, uniqOverlapBases);
cdwQaEnrichSaveToDb(conn, enrich, "cdwQaEnrich", 128);
cdwQaEnrichFree(&enrich);
}
genomeRangeTreeFree(&sampleGrt);
hashElFreeList(&chromList);
}
void outputOverlappingGrt(struct bed *chiaList, struct genomeRangeTree *grt,
double *out1, double *out2)
{
int chiaIx = 0;
struct bed *chia;
for (chia = chiaList; chia != NULL; chia = chia->next)
{
int blockStart = chia->chromStart;
int blockSize = chia->blockSizes[0];
int blockEnd = blockStart + blockSize;
int overlap = genomeRangeTreeOverlapSize(grt, chia->chrom, blockStart, blockEnd);
out1[chiaIx] = (double)overlap/blockSize;
blockStart = chia->chromStart + chia->chromStarts[1];
blockSize = chia->blockSizes[1];
blockEnd = blockStart + blockSize;
overlap = genomeRangeTreeOverlapSize(grt, chia->chrom, blockStart, blockEnd);
out2[chiaIx] = (double)overlap/blockSize;
++chiaIx;
}
}
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);
}
