Secondary and supplementary reads

[lindenb]

Hi, unless I'm wrong, supplementary and seconday alignments are not ignored in your code.

https://github.com/zd1/telseq/blob/master/src/Telseq/telseq.cpp#L275

shouldn't you remove them ?

Furthermore, speed could be improved by using references instead of values:

e.g:

int countMotif(std::string &read, std::string& pattern, std::string& pattern_revcomp){

instead of

int countMotif(std::string &read, std::string pattern, std::string pattern_revcomp){