#'@title Generate hisat2 command in R
#'
#'@examples
#'library(RbashGEO)
#'library(dplyr)
#'Coldata_new <- read.csv("./Coldata_M14new.csv")
#'
#'mapply(
#' function(x,y){
#' Rhisat2(Fastq_file_name = x,
#' Paired = y,
#' parallel_num = 1,
#' Fastq_directory = getwd()) %>% Rnohup(.,paste0(x,"_hisat2"))},
#' Coldata_new$SRR_RUN,
#' (Coldata_new$Lib == "Paired")
#')
#'
#'@seealso \code{\link{Check_hisat2_reports}}
#'
#'
#'@export
#'
Rhisat2 <- function (Fastq_file_name = "SRR1234567",
indx_directory = "/home/zhen/hisat2_idx/hg19/genome",
Fastq_directory = ".",
Paired = F,
trim_5 = NULL,
trim_3 = NULL,
parallel_num = 8,
Fastq_file_end = ".fastq",
output_name = Fastq_file_name,
tune_Mismatch_MX = NULL,
tune_Mismatch_MN = NULL)
{
Fastq_directory = gsub("/$","",Fastq_directory)
if (Paired) {
input_argument = paste0( " -1 ",Fastq_directory,"/",Fastq_file_name,"_1",Fastq_file_end," -2 ",Fastq_directory,"/",Fastq_file_name,"_2",Fastq_file_end)
}
else {
input_argument = paste0( " -U ",Fastq_directory,"/",Fastq_file_name,Fastq_file_end)
}
trim_argument = ifelse(is.null(trim_5),"",paste0(" -5 ",trim_5," -3 ",trim_3))
mismatch_argument = ifelse(is.null(tune_Mismatch_MX),"",paste0(" --mp ",tune_Mismatch_MX,",",tune_Mismatch_MN))
output_argument = paste0(" -S ",output_name,".sam")
paste0("hisat2 -p ",parallel_num, trim_argument, mismatch_argument," --no-unal -x ",indx_directory,input_argument,output_argument)
}
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