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# some auxiliary functions from package 'seqminer' (c) 2015
#' Check if the input is url e.g. http:// or ftp://
#' @param fileName character vector
#' @keywords internal
isURL <- function(fileName) {
if (grepl(pattern = "^http://", fileName) ||
grepl(pattern = "^ftp://", fileName) ) {
return(TRUE)
}
return(FALSE)
}
local.file.exists <- function(fileName) {
if (isURL(fileName)) {
return(TRUE)
}
return(file.exists(fileName))
}
#' Check input file has tabix index
#'
#' @param fileName character vector, representing file names an input file name
#' @return TRUE if an index file with ".tbi" or "bci" exists, and created later than VCF/BCF file
#' @keywords internal
hasIndex <- function(fileName) {
if (isURL(fileName)) {
return(TRUE)
}
endsWith <- function(i, pattern = NULL) {
if (is.null(pattern)) {
return(FALSE)
}
if (length(fileName) != 1) {
stop("hasIndex() only take vector of length 1.")
return (FALSE)
}
p <- paste(pattern, "$", sep = "")
if (length(grep(x=i, pattern=p)) != 1) {
return (FALSE)
}
return (TRUE)
}
## handle VCF
fIndex <- NULL
if (endsWith(fileName, ".vcf")) {
stop(gettextf("Input file is not bgzip compressed. Please use: [ bgzip %s ]", fileName))
return (FALSE)
}
if (endsWith(fileName, ".vcf.gz")) {
fIndex <- paste(fileName, ".tbi", sep = "")
if (!file.exists(fIndex)) {
stop(gettextf("Cannot find index file (you can create it using: [ tabix -p vcf %s ])" , fileName))
return (FALSE)
}
}
## handle BCF
if (endsWith(fileName, ".bcf")) {
stop(gettextf("Input file is not bgzip compressed. Please use: [ bgzip %s ]", fileName))
return (FALSE)
}
if (endsWith(fileName, ".bcf.gz")) {
fIndex <- paste(fileName, ".bci", sep = "")
if (!file.exists(fIndex)) {
stop(gettextf("Cannot find index file (you can create it using: [ bcftools index %s ])" , fileName))
return (FALSE)
}
}
## Check index file
if (is.null(fIndex)) {
stop(gettextf("Cannot guess a valid tabix index, did your file have suffix: .vcf, .vcf.gz, .bcf, or .bcf.gz ?"))
return (FALSE)
}
if (!file.exists(fIndex)) {
stop(gettextf("The index file [ %s ] does not exists.", fIndex))
return (FALSE)
}
## Check index file timestamp
time.data <- file.info(fileName)$mtime
time.index <- file.info(fIndex)$mtime
if (time.data > time.index) {
stop(gettextf("Index file [ %s ] is older than data file [ %s ].", fIndex, fileName))
return(FALSE)
}
return (TRUE)
}
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