Commit 15e0f4e1 authored by Mikaël Salson's avatar Mikaël Salson

AffectAnalyser: Retrieve depending on the spaced seed not only the substring

parent f0aacfc3
......@@ -208,7 +208,7 @@ template <class T>
string KmerAffectAnalyser<T>::toString() const{
string kmer;
for (size_t i = 0; i < affectations.size(); i++)
kmer += affectations[i].toString()+": "+seq.substr(i,kms.getK())+"\n";
kmer += affectations[i].toString()+": "+spaced(seq.substr(i,kms.getS()), kms.getSeed())+"\n";
return kmer;
}
......
......@@ -75,6 +75,11 @@ public:
*/
int getS() const;
/**
* @return the seed used
*/
string getSeed() const;
/**
* @param seq: a sequence
* @param no_revcomp: force not to revcomp the sequence, even if
......@@ -188,6 +193,11 @@ int IKmerStore<T>::getS() const {
return s;
}
template<class T>
string IKmerStore<T>::getSeed() const {
return seed;
}
template<class T>
vector<T> IKmerStore<T>::getResults(const string &seq, bool no_revcomp) {
if ((int)seq.length() < s - 1) {
......
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