// Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#include <Rcpp.h>

using namespace Rcpp;

#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// pairwiseMutMatrixRcpp
List pairwiseMutMatrixRcpp(NumericVector informative_pos, StringMatrix mutMtx, NumericMatrix motifMtx);
RcppExport SEXP _scoper_pairwiseMutMatrixRcpp(SEXP informative_posSEXP, SEXP mutMtxSEXP, SEXP motifMtxSEXP) {
BEGIN_RCPP
    Rcpp::RObject rcpp_result_gen;
    Rcpp::RNGScope rcpp_rngScope_gen;
    Rcpp::traits::input_parameter< NumericVector >::type informative_pos(informative_posSEXP);
    Rcpp::traits::input_parameter< StringMatrix >::type mutMtx(mutMtxSEXP);
    Rcpp::traits::input_parameter< NumericMatrix >::type motifMtx(motifMtxSEXP);
    rcpp_result_gen = Rcpp::wrap(pairwiseMutMatrixRcpp(informative_pos, mutMtx, motifMtx));
    return rcpp_result_gen;
END_RCPP
}
// countSeqsWithInvalidBases_rcpp
int countSeqsWithInvalidBases_rcpp(CharacterVector seqs);
RcppExport SEXP _scoper_countSeqsWithInvalidBases_rcpp(SEXP seqsSEXP) {
BEGIN_RCPP
    Rcpp::RObject rcpp_result_gen;
    Rcpp::RNGScope rcpp_rngScope_gen;
    Rcpp::traits::input_parameter< CharacterVector >::type seqs(seqsSEXP);
    rcpp_result_gen = Rcpp::wrap(countSeqsWithInvalidBases_rcpp(seqs));
    return rcpp_result_gen;
END_RCPP
}
// fastDist_rcpp
IntegerMatrix fastDist_rcpp(CharacterVector seqs);
RcppExport SEXP _scoper_fastDist_rcpp(SEXP seqsSEXP) {
BEGIN_RCPP
    Rcpp::RObject rcpp_result_gen;
    Rcpp::RNGScope rcpp_rngScope_gen;
    Rcpp::traits::input_parameter< CharacterVector >::type seqs(seqsSEXP);
    rcpp_result_gen = Rcpp::wrap(fastDist_rcpp(seqs));
    return rcpp_result_gen;
END_RCPP
}

static const R_CallMethodDef CallEntries[] = {
    {"_scoper_pairwiseMutMatrixRcpp", (DL_FUNC) &_scoper_pairwiseMutMatrixRcpp, 3},
    {"_scoper_countSeqsWithInvalidBases_rcpp", (DL_FUNC) &_scoper_countSeqsWithInvalidBases_rcpp, 1},
    {"_scoper_fastDist_rcpp", (DL_FUNC) &_scoper_fastDist_rcpp, 1},
    {NULL, NULL, 0}
};

RcppExport void R_init_scoper(DllInfo *dll) {
    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
    R_useDynamicSymbols(dll, FALSE);
}
