R/index_conda.R

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

#' Tabix-index a file: conda
#' 
#' Tabix-index a tabular summary statistics file.
#' @inheritParams construct_query
#' @inheritParams index
#' @keywords internal
index_conda <- function(bgz_file,
                        chrom_i,
                        start_i,
                        end_i,
                        comment_char,
                        skip_lines=0,
                        force_new=FALSE,
                        conda_env="echoR_mini",
                        verbose=TRUE){   
    messager("Tabix-indexing file using: conda",v=verbose) 
    conda_env <- echoconda::yaml_to_env(yaml_path = conda_env,
                                        verbose = verbose)
    tabix <- echoconda::find_packages(packages = "tabix",
                                     conda_env = conda_env,
                                     return_path = TRUE,
                                     verbose = verbose)
    cmd2 <- paste(tabix[[1]],
                  # Force overwrite of .tbi index file
                  if(force_new) "-f" else NULL,
                  "-S",skip_lines, 
                  "-s",chrom_i,
                  "-b",start_i,
                  "-e",end_i,
                  "-c",comment_char,
                  bgz_file)
    echoconda::cmd_print(cmd2, verbose=verbose)
    system(cmd2) 
}