In knausb/vcfR_docs: Documentation For VcfR

#include <Rcpp.h>
// [[Rcpp::export]]
Rcpp::NumericMatrix myBinner(Rcpp::NumericVector myVect, float bin_width = 0.2){

  int i = 0;
  int j = 0;
  int nbins = 1/bin_width;
  Rcpp::NumericMatrix breaks( nbins, 4 );
  int multiplier = 1000;
  Rcpp::IntegerMatrix intBreaks( nbins, 4 );

  Rcpp::StringVector colnames(4);
  colnames(0) = "START";
  colnames(1) = "MID";
  colnames(2) = "END";
  colnames(3) = "COUNT";
  Rcpp::colnames(breaks) = colnames;
  Rcpp::colnames(intBreaks) = colnames;

//  Rcpp::IntegerVector counts(nbins);

  breaks(0,0) = 0;
  breaks(0,1) = bin_width/2;
  breaks(0,2) = bin_width;
  intBreaks(0,0) = 0;
  intBreaks(0,1) = (bin_width/2) * multiplier;
  intBreaks(0,2) = bin_width * multiplier;

  for(i=1; i<breaks.nrow(); i++){
    breaks(i,0) = breaks(i-1,0) + bin_width;
    breaks(i,1) = breaks(i-1,1) + bin_width;
    breaks(i,2) = breaks(i-1,2) + bin_width;

    intBreaks(i,0) = intBreaks(i-1,0) + bin_width * multiplier;
    intBreaks(i,1) = intBreaks(i-1,1) + bin_width * multiplier;
    intBreaks(i,2) = intBreaks(i-1,2) + bin_width * multiplier;
  }

  Rcpp::Rcout << "\nBinning!\n\n";

  for(i=0; i<myVect.size(); i++){
    int intQuery = myVect(i) * multiplier;
    j = 0;
    if( intQuery >= intBreaks(j,0) & intQuery <= intBreaks(j,2) ){
//    if( myVect(i) >= breaks(j,0) & myVect(i) <= breaks(j,2) ){
      Rcpp::Rcout << "Binned: " <<  myVect(i) << " is >= " << breaks(j,0) << " & <= " << breaks(j,2) << "\n";
      breaks(j,3) = breaks(j,3) + 1;
    }
    for(j=1; j<breaks.nrow(); j++){
      if( intQuery > intBreaks(j,0) & intQuery <= intBreaks(j,2) ){
//      if( myVect(i) >= breaks(j,0) & myVect(i) <= breaks(j,2) ){
        Rcpp::Rcout << "Binned: " <<  myVect(i) << " is > " << breaks(j,0) << " & <= " << breaks(j,2) << "\n";
        breaks(j,3) = breaks(j,3) + 1;
      }
    }

  }

  return(breaks);  
}

set.seed(9)
#x <- runif(n=4)
#
binWidth <- 0.02
#binWidth <- 0.2
x <- c(0, 0.2, 0.4, 0.8, 1.0)
counts <- myBinner(x, binWidth)

myHist <- hist(x, plot = FALSE, breaks = seq(0,1,by=binWidth))
#
cbind(counts, myHist$counts)

#include <Rcpp.h>
// [[Rcpp::export]]
void myFunction( double bin_width = 0.2 ){
  int nbins = 1/bin_width;
  int i = 0;

  Rcpp::NumericVector query(1);
//  query(0) = 0.1;
//  query(0) = 0.2;
  query(0) = 0.4;

  Rcpp::NumericVector breaks( nbins + 1 );
  breaks(0) = 0;
  for(i=1; i<breaks.size(); i++){
    breaks(i) = breaks(i-1) + bin_width;
  }

  Rcpp::Rcout << "Testing: \n";

  for(i=0; i < breaks.size() - 1; i++){
    if( query(0) > breaks(i) & query(0) <= breaks(i+1) ){
      Rcpp::Rcout << "Binned: " << query(0) << " is > " << breaks(i) << " and <= " << breaks(i+1) << "\n";
    }
  }


}

myFunction( bin_width = 0.2)
myFunction( bin_width = 0.1)
myFunction( bin_width = 0.05)
myFunction( bin_width = 0.02)
myFunction( bin_width = 0.01)

#include <Rcpp.h>
// [[Rcpp::export]]
void myIntFunction( double bin_width = 0.2 ){
  int nbins = 1/bin_width;
  int i = 0;
  int multiplier = 1000;

  Rcpp::NumericVector query(1);
//  query(0) = 0.1;
//  query(0) = 0.2;
  query(0) = 0.4;

  // Initialize breaks.
  Rcpp::NumericVector breaks( nbins + 1 );
  Rcpp::IntegerVector intBreaks( nbins + 1 );
  breaks(0) = 0;
  intBreaks(0) = 0;
  for(i=1; i<breaks.size(); i++){
    breaks(i) = breaks(i-1) + bin_width;
    intBreaks(i) = intBreaks(i-1) + bin_width * multiplier;
  }

  Rcpp::Rcout << "Testing: \n";

  for(i=0; i < breaks.size() - 1; i++){
//    Rcpp::as< int >(StringV(i));
    int intQuery = query(0) * multiplier;
//    intQuery = intQuery * multiplier;

    if( intQuery > intBreaks(i) & intQuery <= intBreaks(i+1) ){
//    if( query(0) > breaks(i) & query(0) <= breaks(i+1) ){
      Rcpp::Rcout << "Binned: " << query(0) << " is > " << breaks(i) << " and <= " << breaks(i+1) << "\n";
    }
  }

}

myIntFunction( bin_width = 0.2)
myIntFunction( bin_width = 0.1)
myIntFunction( bin_width = 0.05)
myIntFunction( bin_width = 0.02)
myIntFunction( bin_width = 0.01)