load BCs for error correct

correct_UB_tags_new <- function(inbamfile,n){

  mm_path <- paste0(opt$out_dir,"/zUMIs_output/molecule_mapping/",n,".")

  outbamfile <-paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.UBcorrected.sorted.bam")

  bcpath <- paste0(opt$out_dir,"/zUMIs_output/",opt$project,"kept_barcodes_binned.txt")

  bcpath <- paste0(opt$out_dir,"/zUMIs_output/",opt$project,"kept_barcodes.txt")

  use_threads <- opt$num_threads

  pypath <- paste0(opt$zUMIs_directory,"/correct_UBtag.py")

  UBcmd <- paste("python3", pypath,

# Pipeline to run UMI-seq analysis from fastq to read count tables.

# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann

# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

vers=2.9.4f

vers=2.9.4g

currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/main/zUMIs.sh | grep '^vers=' | cut -f2 -d "=")

if [ "$currentv" != "$vers" ] ; then

    echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";