R/Rsamtools_view.R

In ZhenWei10/RbashGEO: GEO raw data processing in bash.

#'@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")
}