R/hail_read.R

In r-spark/sparkhail: A 'Sparklyr' Extension for 'Hail'

#' Read a MatrixTable
#' 
#' Read and create a MatrixTable object, it is necessary to convert the data in 
#' dataframe using \code{\link[sparkhail]{hail_dataframe}}.
#' 
#' @details 
#' A hail \href{https://hail.is/docs/0.2/overview/matrix_table.html?highlight=matrixtable}{MatrixTable} 
#' is a standard data structure in hail framework. A MatrixTable consists of four
#' components: 
#' 
#' \itemize{
#'   \item{a two-dimensional matrix of entry fields where each entry is indexed by row 
#'   key(s) and column key(s)}
#'   \item{a corresponding rows table that stores all of the row fields that are 
#'   constant for every column in the dataset}
#'   \item{a corresponding columns table that stores all of the column fields that
#'    are constant for every row in the dataset}
#'   \item{a set of global fields that are constant for every entry in the dataset}  
#' }
#' 
#' You can see the MatrixTable structure using \code{\link[sparkhail]{hail_describe}}.
#' 
#' @param hl A hail context object. Create one using \code{hail_context()}.
#' @param path A string with the path to MatrixTable folder 
#' @return hail_matrix_table
#' @export
hail_read_matrix <- function(hl, path){
  
  mt <- sparklyr::invoke_static(sparklyr::spark_connection(hl), 
                                "is.hail.variant.MatrixTable", "read",
                                hl, path, FALSE, FALSE)
  
  class(mt) <- c(class(mt), "hail_matrix_table")
  mt
}