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#include <cstdint>
#include <iostream>
#include <vector>
#include <pbdata/DNASequence.hpp>
#include <pbdata/NucConversion.hpp>
#include <pbdata/SeqUtils.hpp>
#include <pbdata/utils.hpp>
template <typename T_Sequence>
int OnlyACTG(T_Sequence &seq)
{
DNALength p;
for (p = 0; p < seq.length; p++) {
if (ThreeBit[seq.seq[p]] > 3) return 0;
}
return 1;
}
template <typename T_Sequence>
DNALength CountMasked(T_Sequence &seq)
{
DNALength p;
DNALength nMasked = 0;
for (p = 0; p < seq.length; p++) {
if ((seq.seq[p] >= 'a' and seq.seq[p] <= 'z') or seq.seq[p] == 'N') {
nMasked++;
}
}
return nMasked;
}
template <typename T_Sequence>
int CountNotMasked(T_Sequence &seq)
{
int nUnmasked = 0;
for (unsigned p = 0; p < seq.length; p++) {
if (seq.seq[p] == 'A' or seq.seq[p] == 'C' or seq.seq[p] == 'G' or seq.seq[p] == 'T') {
nUnmasked++;
}
}
return nUnmasked;
}
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