R/decompress.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Decompress a file
#' 
#' Decompress a gzipped (.gz) or bgzipped (.bgz) file. 
#' 
#' @param path_formatted Path to compressed file. 
#' @inheritParams get_example_gwas
#' @inheritParams R.utils::gunzip
#' @returns Path to decompressed file.
#' 
#' @keywords internal
decompress <- function(path_formatted,
                       remove = FALSE,
                       overwrite = TRUE,
                       storage_dir = tempdir(),
                       verbose = TRUE) {
  # devoptera::args2vars(decompress)

  if (grepl("\\.gz$|\\.bgz$",path_formatted)) {
      #### Decompress gzipped file #####
      destname <- file.path(
          storage_dir,
          gsub("\\.gz|\\.bgz", "", basename(path_formatted))
      )
      messager("Saving decompressed copy of path_formatted ==> ", destname,
               v=verbose)
      if (!file.exists(destname) || isTRUE(overwrite)) {
          path_formatted2 <- R.utils::gunzip(
              path_formatted,
              destname = destname,
              remove = remove,
              overwrite = overwrite
          )
      } else {
          path_formatted2 <- destname
      }
  } else if (endsWith(path_formatted, ".bgz")) {
      #### Decompress bgzipped file #####
      destname <- file.path(
          storage_dir,
          sub(".bgz", "", basename(path_formatted))
      )
      messager("Saving decompressed copy of path_formatted ==> ", destname,
               v=verbose)
      if (!file.exists(destname) | overwrite) {
          path_formatted2 <- R.utils::bunzip2(path_formatted,
              destname = destname,
              remove = remove,
              overwrite = overwrite
          )
      } else {
          path_formatted2 <- destname
      }
  } else {
      path_formatted2 <- path_formatted
  }
  return(as.character(path_formatted2))
}