R/index_seqminer.R

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

#' Tabix-index a file: \pkg{seqminer}
#' 
#' Tabix-index a tabular summary statistics file.
#' @inheritParams construct_query
#' @inheritParams index
#' @keywords internal
index_seqminer <- function(bgz_file,
                           chrom_i,
                           start_i,
                           end_i,
                           comment_char,
                           skipLines=0,
                           verbose=TRUE){
    messager("Tabix-indexing file using: seqminer",v=verbose) 
    requireNamespace("seqminer") 
    seqminer::tabix.createIndex(
        bgzipFile = bgz_file,
        sequenceColumn = chrom_i,
        startColumn = start_i,
        endColumn = end_i,  
        metaChar = comment_char,
        skipLines = skipLines
    )  
}