#' Is natural number
 #' @return Logical
 #' @keywords  internal
 
 isNaturalNumber <- function(x) {
 
 
 if (length(x) != length(unlist(x))) {
     return(FALSE)
 }
 x <- unlist(x)
 
 
 if (any(is.na(x))) {
     return(FALSE)
 }
 
 if (!is.numeric(x)) {
     return(FALSE)
 }
 
 if (!all(x == round(x) & x > 0)) {
     return(FALSE)
 }
 TRUE
 }
 
 
 #' ASCII to integer
 #' @return  Integer
 #' @keywords internal
 
 asc2int <- function(x) strtoi(charToRaw(x), 16L)
 
 

 #' Integer to ASCII 

 #' @return ASCII character
 #' @keywords internal
 
 int2asc <- function(n) rawToChar(as.raw(n))
 
 

 #' Check quality encoding
 #' @param x Quality values

 #' @param custom custom encoding from the following:
 #' 
 #' 'Sanger' --------> expected range: [0, 40]
 #' 
 #' 'Illumina1.8' --------> expected range: [0, 41]
 #' 
 #' 'Illumina1.5' --------> expected range: [0, 40]
 #' 
 #' 'Illumina1.3' --------> expected range: [3, 40]
 #' 
 #' 'Solexa' --------> expected range: [-5, 40]
 #' 
 #' @examples
 #' 
 #' require(Biostrings)
 #' 
 #' x <- list(PhredQuality(0:40), SolexaQuality(-5:40), IlluminaQuality(3:40))
 #' x <- lapply(x, function(i)utf8ToInt(as.character(i)[1]))
 #' lapply(x, check_encoding)
 #'  
 #' SolexaQuality(0:40)
 #' IlluminaQuality(0:40)
 #' @return  List with encoding information
 #' @author Leandro Roser \email{learoser@@gmail.com}
 #' @export
 
 check_encoding <- function(x = NULL, custom = NULL) {
 
 if (!is.null(x) && !is.null(custom)) {
     stop("Either only a set of qualities 
     or a custom encoding must be selected")
 }
 
 
 if (!is.null(custom) && !custom %in% seq_len(5)) {
     stop("argument custom must be in the range [1, 5]")
 }
 
 outFormats <- list(
     A = list(x = "Sanger", y = 1, q = 33, range = "[33 - 73]"), 
     B = list(x = "Illumina 1.8+", y = 2, q = 33, range = "[33; 74]"), 
     C = list(x = "Illumina 1.5+", y = 3, q = 64, range = "[66; 104]"), 
     D = list(x = "Illumina 1.3+", y = 4, q = 64, range = "[64; 104]"),
     E = list(x = "Solexa", y = 5, q = 64, range = "[59; 104]"))
 
 if (!is.null(x)) {
     xmin <- min(x, na.rm = TRUE)
     xmax <- max(x, na.rm = TRUE)
 
 if (xmin < 33 || xmax > 104) {
     stop(paste0("Quality values corrupt. Found [min = ", 
         xmin, " max=", xmax, "],  
     but a range between [33; 104] was expected\n"))
 }
 
 if (xmin >= 33 && xmax <= 73) 
     out <- outFormats$A  
 else if (xmin >= 33 && xmax <= 74) 
     out <- outFormats$B  
 else if (xmin >= 66 && xmax <= 104) 
     out <- outFormats$C 
 else if (xmin >= 64 && xmax <= 104) 
     out <- outFormats$D 
 else if (xmin >= 59 && xmax <= 104) 
     out <- outFormats$E 
 
 } else {
 if (custom == 1) 
     out <- outFormats$A  
 else if (custom == 2) 
     out <- outFormats$B 
 else if (custom == 3) 
     out <- outFormats$C  
 else if (custom == 4) 
     out <- outFormats$D 
 else if (custom == 5) 
     out <- outFormats$E 
 }
 
 out
 
 }