void RevComplementInPlace(string& seq) {
char c;
int forward_idx = 0;
int backward_idx = seq.size()-1;
while (forward_idx < backward_idx) {
c = seq[forward_idx];
seq[forward_idx] = NucComplement(seq[backward_idx]);
seq[backward_idx] = NucComplement(c);
forward_idx++;
backward_idx--;
}
if (forward_idx == backward_idx)
seq[forward_idx] = NucComplement(seq[forward_idx]);
}
string Realigner::ComplementSequence(string seq, bool reverse) const
{
if (reverse) {
char c;
int forward_idx = 0;
int backward_idx = seq.size()-1;
while (forward_idx < backward_idx) {
c = seq[forward_idx];
seq[forward_idx] = NucComplement(seq[backward_idx]);
seq[backward_idx] = NucComplement(c);
forward_idx++;
backward_idx--;
}
if (forward_idx == backward_idx)
seq[forward_idx] = NucComplement(seq[forward_idx]);
} else {
for (unsigned int i=0; i<seq.size(); i++)
seq[i] = NucComplement(seq[i]);
}
return seq;
}
void ReverseComplement(string &seqContext, string &reverse_complement) {
reverse_complement = seqContext;
for (unsigned i=0;i<seqContext.length(); i++)
reverse_complement[reverse_complement.length()-1-i] = NucComplement(seqContext[i]);
}
void reverseComplement(string s, char * x) {
x[s.length()] = '\0';
for (int i=s.length()-1;i>=0;i--)
x[s.length()-1-i] = NucComplement(s[i]);
}
