static void getFloatArray(struct annoStreamWig *self, struct wiggle *wiggle,
boolean *retRightFail, int *retValidCount, float *vector)
/* expand wiggle bytes & spans to per-bp floats; filter values here! */
{
udcSeek(self->wibFH, wiggle->offset);
UBYTE wigBuf[wiggle->count];
size_t expectedBytes = sizeof(wigBuf);
size_t bytesRead = udcRead(self->wibFH, wigBuf, expectedBytes);
if (bytesRead != expectedBytes)
errnoAbort("annoStreamWig: failed to udcRead %llu bytes from %s (got %llu)\n",
(unsigned long long)expectedBytes, wiggle->file, (unsigned long long)bytesRead);
paranoidCheckSize(self, wiggle);
int i, j, validCount = 0;
for (i = 0; i < wiggle->count; i++)
{
float value;
if (wigBuf[i] == WIG_NO_DATA)
value = NAN;
else
{
value = BIN_TO_VALUE(wigBuf[i], wiggle->lowerLimit, wiggle->dataRange);
if (annoFilterWigValueFails(self->streamer.filters, value, retRightFail))
value = NAN;
else
validCount++;
}
int bpOffset = i * wiggle->span;
for (j = 0; j < wiggle->span; j++)
vector[bpOffset + j] = value;
}
if (retValidCount != NULL)
*retValidCount = validCount;
}
static struct annoRow *asbwNextRow(struct annoStreamer *sSelf, char *minChrom, uint minEnd,
struct lm *callerLm)
/* Return a single annoRow, or NULL if there are no more items. */
{
struct annoStreamBigWig *self = (struct annoStreamBigWig *)sSelf;
if (self->eof)
return NULL;
else if (self->nextInterval == NULL)
{
asbwDoQuery(self, minChrom, minEnd);
if (self->eof)
return NULL;
}
// Skip past any left-join failures until we get a right-join failure, a passing interval, or EOF.
boolean rightFail = FALSE;
struct bbiInterval *startIv = self->nextInterval;
while (annoFilterWigValueFails(sSelf->filters, self->nextInterval->val, &rightFail))
{
if (rightFail)
break;
startIv = self->nextInterval = self->nextInterval->next;
if (self->nextInterval == NULL)
return NULL;
}
char *chrom = sSelf->chrom ? sSelf->chrom : self->queryChrom->name;
if (rightFail)
return annoRowFromContigBbiIntervals(sSelf->name, chrom, startIv, startIv, rightFail,
callerLm);
// Collect up to maxCount contiguous intervals; then make annoRow with vector.
struct bbiInterval *endIv = startIv, *iv;
int maxCount = 16 * 1024, count;
for (iv = startIv->next, count = 0; iv != NULL && count < maxCount; iv = iv->next, count++)
{
if (annoFilterWigValueFails(sSelf->filters, iv->val, &rightFail))
break;
if (iv->start == endIv->end)
endIv = iv;
else
break;
}
// If there's a query region and we have reached the end of its intervals, we're done.
if (sSelf->chrom != NULL && endIv->next == NULL)
self->eof = TRUE;
self->nextInterval = endIv->next;
return annoRowFromContigBbiIntervals(sSelf->name, chrom, startIv, endIv, rightFail, callerLm);
}
