#include <alignment/algorithms/anchoring/FindMaxInterval.hpp>

unsigned int NumRemainingBases(DNALength curPos, DNALength intervalLength)
{
    if (curPos > intervalLength) {
        return 0;
    } else {
        return intervalLength - curPos;
    }
}

IntervalSearchParameters::IntervalSearchParameters()
{
    advanceHalf = false;
    globalChainType = 0;
    maxPValue = log(0.1);
    aboveCategoryPValue = 0;
    warp = true;
    fastMaxInterval = false;
    aggressiveIntervalCut = false;
    verbosity = 0;
    ddPValueThreshold = -500;
}