#include "DropletUtils.h"
#include "H5Cpp.h"
#include <cstdint> 

SEXP get_cell_barcodes(SEXP _fname, SEXP _dname, SEXP _barcodelen) {
    BEGIN_RCPP
    Rcpp::StringVector fname(_fname);
    Rcpp::StringVector dname(_dname);
    if (fname.size()!=1) {
        throw std::runtime_error("file name should be a string");
    }
    if (dname.size()!=1) {
        throw std::runtime_error("dataset name should be a string");
    }

    // Setting the file input parameters.
    std::string curfile=Rcpp::as<std::string>(fname[0]);
    std::string curdata=Rcpp::as<std::string>(dname[0]);
    H5::H5File h5file(curfile.c_str(), H5F_ACC_RDONLY);
    H5::DataSet h5data = h5file.openDataSet(curdata.c_str());
    
    if (h5data.getTypeClass()!=H5T_INTEGER) {
        throw std::runtime_error("cell barcodes should be encoded as integers");
    }

    // Determining the dimensions.
    H5::DataSpace dataspace = h5data.getSpace();
    if (dataspace.getSimpleExtentNdims()!=1) {
        throw std::runtime_error("cell barcodes should be a one-dimensional array");
    }
    hsize_t dims_out;
    dataspace.getSimpleExtentDims(&dims_out, NULL);

    // Extracting the data.
    H5::DataSpace memspace(1, &dims_out);
    memspace.selectAll();
    dataspace.selectAll();
    std::vector<std::uint64_t> encoded(dims_out);
    h5data.read(encoded.data(), H5::PredType::NATIVE_UINT64, memspace, dataspace);
   
    // Guessing the barcode length. 
    int blen=0;
    if (_barcodelen==R_NilValue) {
        if (encoded.size()) { 
            blen=std::ceil(std::log(*std::max_element(encoded.begin(), encoded.end()))/std::log(4));
        }
    } else {
        blen=check_integer_scalar(_barcodelen, "barcode length");
    }

   // Iterating across the output and taking pairs of bits.
    Rcpp::StringVector output(dims_out);
    auto oIt=output.begin();
    std::vector<char> ref(blen+1, '\0');   
    const char* bases="ACGT";

    for (const auto& enc : encoded) {
        for (int pos=0; pos<blen; ++pos) {
            auto leftover=(enc >> 2*pos) & 0x3;
            ref[blen - pos - 1]=bases[leftover];
        }

        (*oIt)=Rcpp::String(ref.data());
        ++oIt;
    }

    return output;    
    END_RCPP
}