R/allStatics.r

In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

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##  Project   :   seqTools                                                   ##
##  Created   :   26.August.2013                                             ##
##  Author    :   W. Kaisers                                                 ##
##  File      :   allStatics.r                                               ##
##  Content   :   All static variables and (not directly object related )    ##
##                function declarations                                      ##
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## Global variables:
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strandlevels <- c("+", "-", "*")
iupac_chars <- c('a', 'c', 'g', 't', 'u', 'r', 'y', 's', 'w', 'k', 'm', 'b',
                  'd', 'h', 'v', 'n', '.', '-', '=')

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## Although static array sizes would allow larger k (e.g. 15: 8 GB RAM), 
## exponential increase in run-time restricts usability to k values in 1:12
## 4^12 = 16.777.216 possible combinations.
## 'Hard' coded (in stat_defs.h: 15)
max_k <- 12
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## End global variables
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## Some useful functions for work with phred's
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char2ascii <- function(c){ strtoi(charToRaw(c), base = 16L) }
ascii2char <- function(x, multiple = FALSE){ rawToChar(as.raw(x), 
                                  multiple = multiple) }

phredTable <- function(phred = 0:93) {
  if(!is.numeric(phred))
    stop("phred must be numeric.")
  phred <- sort(unique(as.integer(phred)))
  if( (phred[1] < 0) || (max(phred) > 93) )
    stop("Only phred values in 0:93 are allowed.")
  
  ascii <- phred + 33
  return(data.frame(ascii = ascii, phred = phred,
                    char = ascii2char(ascii, multiple=TRUE)))
}
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# unexported functions,  do not check for x
rel_int  <- function(x) {return(.Call("rel_int", x, PACKAGE="seqTools"))}
rel_real <- function(x) {return(.Call("rel_real", x, PACKAGE="seqTools"))}

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enlargeIntMat <- function(x, newDim){
  if(!is.matrix(x))
    stop("x must be matrix.")
  if(!is.numeric(newDim))
    stop("newDim must be numeric.")
  newDim <- as.integer(newDim)
  if(length(newDim) != 2)
    stop("newDim must have length 2.")
  return(.Call("r_enlarge_int_mat", x, newDim, PACKAGE="seqTools"))
}

kMerIndex <- function(kMers, k=nchar(kMers)[1], base = 1)
{
  if(!is.character(kMers))
    stop("kMers must be character.")
  if(!is.numeric(k))
    stop("k must be numeric.")
  k <- as.integer(k)
  if(k<0 || k> max_k)
    stop("k must be in range 0,  ... , ", max_k, ".")
  if(!all(nchar(kMers) == k))
    stop("All kMers must have k characters!")
  if(!is.numeric(base))
    stop("base must be numeric")
  if(length(base)>1)
    stop("base must have length 1.")
  base<-as.integer(base)
  if(!(base %in% 0:1))
    stop("base must be 0 or 1.")
  
  return(.Call("get_Kmer_Index", kMers, k, PACKAGE="seqTools")+base)
}

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## END OF FILE
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