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#include "ClusterProbability.hpp"
#include <cassert>
#include <math.h>
float ComputeAnchorProbability(float pMatch, int minAnchorLength) {
assert(minAnchorLength >= 0);
assert(pMatch < 1.00001 and pMatch > 0);
int i;
float totalProbability = 0.0;
float pMisMatch = 1 - pMatch;
for (i = 0; i < minAnchorLength; i++) {
totalProbability += pMatch * pMisMatch;
pMatch *= pMatch;
}
return 1 - totalProbability;
}
float ComputeExpectedAnchorLength(float pMatch, int minAnchorLength,
float pAnchor) {
int i = 0;
for (i = 0; i < minAnchorLength; i++) {
pMatch *= pMatch;
}
float pMismatch = 1 - pMatch;
float pValueEpsilon = 0.000000001;
float expAnchorLength = 0;
while(pMatch*pMismatch > pValueEpsilon) {
expAnchorLength += i * pMatch*pMismatch/pAnchor;
pMatch *= pMatch;
}
return expAnchorLength;
}
float AnchorBasesPerRead(int readLength, float pAnchor) {
return pAnchor * readLength;
}
float AnchorBasesPerReadSigma(float expAnchorBasesPerRead) {
// Assume exponential distribution:
return sqrt(expAnchorBasesPerRead);
}
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