#'@title Samtools views in R to filter multiple alignments
#'
#'@examples
#'sam_filenames <- gsub(".sam","",grep(".sam$",list.files(),value = T) )
#'sapply(
#' sam_filenames,
#' function(x){
#' Rsamtools_view(x,flag_filter = 2816) %>% Rnohup(.,paste0(x,"_samfilter") )
#' }
#')
#
#'@export
#'
#'
Rsamtools_view = function(sam_name, sam_directory = ".", sam_end = ".sam", parallel_num = 8,flag_filter = 2816) {
sam_directory = gsub("/$", "", sam_directory)
paste0("samtools view -@ ", parallel_num, " -F ", flag_filter,
" -q 30 -Sb ", sam_directory, "/", sam_name, sam_end,
" -o ", sam_directory, "/", sam_name, ".bam")
}
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