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#include <alignment/statistics/LookupAnchorDistribution.hpp>
int LookupAnchorDistribution(int readLength, int minMatchLength, int accuracy, float &mn,
float &sdn, float &mnab, float &sdnab)
{
int kIndex, accIndex, lengthIndex;
int returnValue = 0;
// Major index is by accuracy
if (accuracy < PacBio::AnchorDistributionTable::anchorReadAccuracies[0]) {
returnValue = -2;
accuracy = PacBio::AnchorDistributionTable::anchorReadAccuracies[0];
} else if (accuracy >= PacBio::AnchorDistributionTable::anchorReadAccuracies[1]) {
returnValue = 2;
accuracy = PacBio::AnchorDistributionTable::anchorReadAccuracies[1] -
PacBio::AnchorDistributionTable::anchorReadAccuracies[2];
}
accIndex = (((int)accuracy) - PacBio::AnchorDistributionTable::anchorReadAccuracies[0]) /
PacBio::AnchorDistributionTable::anchorReadAccuracies[2];
// middle index is by k
if (minMatchLength < PacBio::AnchorDistributionTable::anchorMinKValues[0]) {
returnValue = -1; // signal too low
minMatchLength = PacBio::AnchorDistributionTable::anchorMinKValues[0];
} else if (minMatchLength >= PacBio::AnchorDistributionTable::anchorMinKValues[1]) {
returnValue = 1; // signal too high
minMatchLength = PacBio::AnchorDistributionTable::anchorMinKValues[1] -
PacBio::AnchorDistributionTable::anchorMinKValues[2]; // max match length
}
kIndex = (minMatchLength - PacBio::AnchorDistributionTable::anchorMinKValues[0]) /
PacBio::AnchorDistributionTable::anchorMinKValues[2];
// last index is by read length
if (readLength < PacBio::AnchorDistributionTable::anchorReadLengths[0]) {
returnValue = -3;
readLength = PacBio::AnchorDistributionTable::anchorReadLengths[0];
} else if (readLength >= PacBio::AnchorDistributionTable::anchorReadLengths[1]) {
returnValue = 3;
readLength = PacBio::AnchorDistributionTable::anchorReadLengths[1] -
PacBio::AnchorDistributionTable::anchorReadLengths[2]; // max read length
}
lengthIndex = (readLength - PacBio::AnchorDistributionTable::anchorReadLengths[0]) /
PacBio::AnchorDistributionTable::anchorReadLengths[2];
int nLengths = (PacBio::AnchorDistributionTable::anchorReadLengths[1] -
PacBio::AnchorDistributionTable::anchorReadLengths[0]) /
PacBio::AnchorDistributionTable::anchorReadLengths[2];
int nAnchors = (PacBio::AnchorDistributionTable::anchorMinKValues[1] -
PacBio::AnchorDistributionTable::anchorMinKValues[0]) /
PacBio::AnchorDistributionTable::anchorMinKValues[2];
int index = accIndex * (nLengths * nAnchors) + kIndex * nLengths + lengthIndex;
mn = PacBio::AnchorDistributionTable::meanNumAnchors[index];
sdn = PacBio::AnchorDistributionTable::sdNumAnchors[index];
mnab = PacBio::AnchorDistributionTable::meanNumAnchorBases[index];
sdnab = PacBio::AnchorDistributionTable::sdNumAnchorBases[index];
return returnValue;
}
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