threading of umitools

  #useIntrons = ifelse(opt$counting_opts$umi_tools == "exon", "--use-introns", "")

  useIntrons = ifelse(opt$counting_opts$introns, "--use-introns", "")

  setLayout = ifelse(opt$read_layout == "PE", "--paired", "")

  #bamfile <- "/data/home/dietrich/outputNew/inex.sorted.bam"

  chroms_todo <- data.table::fread(cmd = paste(opt$samtools_exec,"idxstats",bamfile), header = F, select = 1)

  chroms_todo <- chroms_todo[V1 != "*"]$V1

  out_dir <- paste0(opt$out_dir,"/umitools/")

  if(!dir.exists(out_dir)){

    dir.create(out_dir)

  }

  umitool_bams <- parallel::mclapply(chroms_todo, function(chr){

    #build command to start umi_tools:

    group_script <- paste0(opt$zUMIs_directory,"/misc/umi-tools/group.py")

  log_outfile <- paste0(opt$out_dir,"/",opt$project,".umi_tools_logfile.txt")

  outfile <- paste0(opt$out_dir,"/",opt$project, ".filtered.tagged.Aligned.out.UMIcorrected.bam")

  parameters <- paste("-I",bamfile,"--output-bam","-L",log_outfile ,useIntrons, "--extract-umi-method=tag", "--umi-tag=UB:Z:", "--cell-tag=BC:Z:", "--per-cell", "--umi-group-tag=XX", "--per-gene", "--gene-tag=GE:Z:", ">", outfile)

    log_outfile <- paste0(out_dir,opt$project,".umi_tools_logfile.",chr,".txt")

    outfile <- paste0(out_dir,opt$project, ".filtered.tagged.Aligned.out.UMIcorrected.",chr,".bam")

    parameters <- paste("-I",bamfile,"--output-bam","-L",log_outfile,"--chrom", chr, useIntrons, "--extract-umi-method=tag", "--umi-tag=UB:Z:", "--cell-tag=BC:Z:", "--per-cell", "--umi-group-tag=XX", "--per-gene", "--gene-tag=GE:Z:", ">", outfile)

   #,"--unmapped-reads=output"

    umi_tools_command <- paste(opt$python_exec, group_script, parameters)

    #print(umi_tools_command)

    system(umi_tools_command)

    return(outfile)

  }, mc.preschedule = FALSE, mc.cores = opt$num_threads)

  umitool_bams <- unlist(umitool_bams)

  umitool_bams <- paste(umitool_bams, collapse=" ")

  outfile <- paste0(opt$out_dir,"/",opt$project,".filtered.tagged.Aligned.out.UMIcorrected.bam")

  merge_cmd <- paste(opt$samtools_exec,"merge -f -@",opt$num_threads,outfile,umitool_bams)

  system(merge_cmd)

  system(paste("rm",umitool_bams))

  return (outfile)

}