#ifndef DROPLETUTILS_H
#define DROPLETUTILS_H

#include "Rcpp.h"
#include "beachmat/integer_matrix.h"
#include "beachmat/numeric_matrix.h"

#include <algorithm>
#include <deque>
#include <stdexcept>
#include <functional>
#include <cmath>
#include <numeric>

// Functions to be called from R.

extern "C" {

SEXP downsample_matrix(SEXP, SEXP, SEXP);

SEXP downsample_runs(SEXP, SEXP, SEXP, SEXP);


SEXP compute_multinom(SEXP, SEXP, SEXP);

SEXP montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP);

SEXP montecarlo_pval_alpha(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);


SEXP find_swapped(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);


SEXP get_cell_barcodes(SEXP, SEXP, SEXP);

SEXP encode_sequences(SEXP);

SEXP group_cells(SEXP, SEXP);


SEXP load_tenx_to_hdf5(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);

}

// Checking for scalar inputs.

int check_integer_scalar(Rcpp::RObject, const char*);

double check_numeric_scalar(Rcpp::RObject, const char*);

bool check_logical_scalar(Rcpp::RObject, const char*);

#endif