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#include <alignment/algorithms/anchoring/ClusterProbability.hpp>
#include <cassert>
#include <cmath>
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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