small optimization

samples[, sample := tstrsplit(r1, file_delim_r1, keep = 1)][

samples[, sample := tstrsplit(r1, file_delim_r1, keep = 1)][

        , BC := stringi::stri_rand_strings(.N, 8, pattern = "[A-Z]")]

        , BC := stringi::stri_rand_strings(.N, 8, pattern = "[A-Z]")]

outfile_r1 <- paste0(opt$dir,"/reads_for_zUMIs.R1.fastq")

outfile_r1 <- paste0(opt$dir,"/reads_for_zUMIs.R1.fastq.gz")

outfile_r2 <- paste0(opt$dir,"/reads_for_zUMIs.R2.fastq")

outfile_r2 <- paste0(opt$dir,"/reads_for_zUMIs.R2.fastq.gz")

outfile_index <- paste0(opt$dir,"/reads_for_zUMIs.index.fastq")

outfile_index <- paste0(opt$dir,"/reads_for_zUMIs.index.fastq")

for(i in seq(nrow(samples))){

for(i in seq(nrow(samples))){

  system(paste("zcat", paste(opt$dir,samples[i]$r1,sep = "/"), ">>", outfile_r1))

  system(paste("cat", paste(opt$dir,samples[i]$r1,sep = "/"), ">>", outfile_r1))

  if(mode == "PE") system(paste("zcat", paste(opt$dir,samples[i]$r2,sep = "/"), ">>", outfile_r2))

  if(mode == "PE") system(paste("cat", paste(opt$dir,samples[i]$r2,sep = "/"), ">>", outfile_r2))

  system(paste0("zcat ", paste(opt$dir,samples[i]$r1,sep = "/"), " | awk -v bc=\"",samples[i]$BC,"\" '{i++;if(i==1 || i==3){print;}if(i==2){print bc;}if(i==4){i=0;print \"AAAAAAAA\";}}' >> ",outfile_index))

  system(paste0(opt$pigz," -p2 -dc ", paste(opt$dir,samples[i]$r1,sep = "/"), " | awk -v bc=\"",samples[i]$BC,"\" '{i++;if(i==1 || i==3){print;}if(i==2){print bc;}if(i==4){i=0;print \"AAAAAAAA\";}}' | ",opt$pigz," -c -p",opt$threads," >> ",outfile_index))

}

}

system(paste(opt$pigz,"-p",opt$threads,outfile_r1))

#system(paste(opt$pigz,"-p",opt$threads,outfile_r1))

if(mode == "PE") system(paste(opt$pigz,"-p",opt$threads,outfile_r2))

#if(mode == "PE") system(paste(opt$pigz,"-p",opt$threads,outfile_r2))

system(paste(opt$pigz,"-p",opt$threads,outfile_index))

#system(paste(opt$pigz,"-p",opt$threads,outfile_index))

fwrite(samples, file =  paste0(opt$dir,"/reads_for_zUMIs.samples.txt"), quote = F, sep = "\t")

fwrite(samples, file =  paste0(opt$dir,"/reads_for_zUMIs.samples.txt"), quote = F, sep = "\t")

write(samples$BC, file = paste0(opt$dir,"/reads_for_zUMIs.expected_barcodes.txt"))

write(samples$BC, file = paste0(opt$dir,"/reads_for_zUMIs.expected_barcodes.txt"))