inline void VQMCCameraDataLimits::
startLimitComputation(const VQMCChannelData& data)
{
fFoundData = false;
fLimitLo.fValue = 0;
fLimitHi.fValue = 0;
fLimitLo.fType = 0;
fLimitHi.fType = 0;
extendLimits(data);
}
static void processResult(struct hash *chrHash, struct hash *coordHash,
char *accName, unsigned querySize, int partsConsidered)
{
struct hashCookie cookie;
struct hashEl *hashEl;
int highCount = 0;
int secondHighest = 0;
char *ctgName = (char *)NULL;
char *secondHighestName = (char *)NULL;
struct hashEl *coords;
int coordCount;
int i;
unsigned lowMark = BIGNUM;
unsigned highMark = 0;
unsigned range = 0;
struct coordEl *coord;
struct coordEl **coordListPt = (struct coordEl **) NULL;
double *midPoints;
double sum;
double sumData = 0.0;
double sumSquares = 0.0;
double variance;
double stddev;
unsigned median;
unsigned mean;
int strandSum;
/* find highest count chrom name */
cookie=hashFirst(chrHash);
while ((hashEl = hashNext(&cookie)) != NULL)
{
int count = ptToInt(hashEl->val);
verbose(2,"# %s %d\n", hashEl->name, count);
if (count >= highCount)
{
secondHighest = highCount;
if (secondHighestName)
freeMem(secondHighestName);
highCount = count;
if (ctgName)
{
secondHighestName = cloneString(ctgName);
freeMem(ctgName);
}
ctgName = cloneString(hashEl->name);
}
}
verbose(2,"# %s %d highest count, next: %s %d\n", ctgName, highCount, secondHighestName, secondHighest);
if (highCount == 0)
return;
if (highCount == secondHighest)
{
int baseCount0 = 0;
int baseCount1 = 0;
/* Try to break the tie by examining the number of bases covered in
* each and take the one with the most
*/
baseCount0 = countBases(coordHash, ctgName);
baseCount1 = countBases(coordHash, secondHighestName);
if (baseCount0 == baseCount1)
{
verbose(1,"# ERROR TIE for high count %s %d highest count, next: %s %d TIE *\n", ctgName, highCount, secondHighestName, secondHighest);
verbose(1,"# ERROR TIE base count0: %d, base count1: %d\n", baseCount0, baseCount1);
}
else if (baseCount1 > baseCount0) /* switch the names */
{
char *t;
t = cloneString(ctgName);
freeMem(ctgName);
ctgName = cloneString(secondHighestName);
freeMem(secondHighestName);
secondHighestName = cloneString(t);
freeMem(t);
}
}
/* for that highest count chrom, examine its coordinates, find high
* and low */
coords = hashLookup(coordHash, ctgName);
if (coords) coordListPt = coords->val;
else coordListPt = NULL;
if (coordListPt) coord = *coordListPt;
else coord = NULL;
coordCount = 0;
sum = 0.0;
sumData = 0.0;
sumSquares = 0.0;
strandSum = 0;
while (coord != NULL)
{
double midPoint;
if (coord->start < lowMark) lowMark = coord->start;
if (coord->end > highMark) highMark = coord->end;
midPoint = (double) coord->start +
(double)(coord->end - coord->start) / 2.0;
sum += midPoint;
strandSum += coord->strand;
sumData += midPoint;
sumSquares += midPoint * midPoint;
verbose(2,"# %d %s %u - %u %u %c\n", ++coordCount, coord->name, coord->start, coord->end, coord->qSize, (coord->strand == 1) ? '+' : '-');
coord = coord->next;
}
range = highMark - lowMark;
variance = 0.0;
stddev = 0.0;
if (coordCount > 0)
{
unsigned usStdDev;
unsigned startExtended;
unsigned endExtended;
int partsUsed = 0;
mean = (unsigned) (sum / coordCount);
if (coordCount > 1)
{
variance = (sumSquares - ((sumData*sumData)/coordCount)) /
(coordCount - 1);
if (variance > 0.0)
stddev = sqrt(variance);
}
usStdDev = (unsigned) stddev;
verbose(2,"# range: %u:%u = %u, Mean: %u, stddev: %u\n", lowMark, highMark, range, mean, usStdDev);
midPoints = (double *) needMem(coordCount * sizeof(double));
coordListPt = coords->val;
coord = *coordListPt;
i = 0;
while (coord != NULL)
{
midPoints[i++] = (double) coord->start +
(double)(coord->end - coord->start) / 2.0;
coord = coord->next;
}
median = (unsigned) doubleMedian(coordCount, midPoints);
partsUsed = extendLimits(coordListPt, median, querySize,
&startExtended, &endExtended, ctgName, partsConsidered);
verbose(2,
"# qSize: %u, Median: %u implies %u-%u %s\n#\textended to %u-%u\n",
querySize, median, median - (querySize/2), median+(querySize/2),
accName, startExtended, endExtended);
verbose(2,"# %s total parts %d, parts used %d, percent used %% %7.2f\n",
accName, partsConsidered, partsUsed,
100.0 * (double) partsUsed / (double) partsConsidered);
/* if BED output, output the line here, AGP was done in extendLimits */
if (!agp)
{
printf("%s\t%u\t%u\t%s\t%c\n", ctgName, startExtended, endExtended,
accName, strandSum > (coordCount/2) ? '+' : '-');
}
freeMem(midPoints);
}
else
{
verbose(1,"# ERROR %s - no coordinates found ? %s\n", accName, ctgName);
}
/* free the chrom coordinates lists */
cookie=hashFirst(chrHash);
while ((hashEl = hashNext(&cookie)) != NULL)
{
coords = hashLookup(coordHash, hashEl->name);
if (coords) coordListPt = coords->val;
else coordListPt = NULL;
if (coordListPt) coord = *coordListPt;
else coord = NULL;
while (coord != NULL)
{
freeMem(coord->name);
coord = coord->next;
}
if (coordListPt)
slFreeList(coordListPt);
}
freeMem(ctgName);
} /* static void processResult() */
