fix rsamtools error

zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.

## Changelog

06 May 2022: zUMIs2.9.7b: Update loading reads with RSamtools to avoid version-dependent failure caused by "*" for unmapped reads.

16 Jul 2021: zUMIs2.9.7: Change perl [shebang line](https://github.com/sdparekh/zUMIs/issues/261). Change featureCounts settings to assign reads to genes with the longest overlap in case of ambiguous/overlapping annotations. Allow to control the minimum required overlap of reads to genes with a setting `fraction_overlap:` in the counting section.

07 Apr 2021: zUMIs2.9.6: Fixed a potential crash when the input file to the barcode sharing feature does not contain an equal number of columns.

reads2genes_new <- function(featfile, bccount, inex, chunk, cores, keepUnassigned = FALSE){

  chunk_bcs <- bccount[chunkID==chunk]$XC

  idxstats <- Rsamtools::idxstatsBam(featfile)

  if("*" %in% idxstats$seqnames){

    idxstats <- idxstats[idxstats$seqnames != "*", ]

    idxstats$seqnames <- as.character(idxstats$seqnames)

  }

  taglist <- c("BC", "UB","GE")

  if(inex){

    taglist <- c(taglist, "GI")

setwd(opt$out_dir)

source(paste0(opt$zUMIs_directory,"/barcodeIDFUN.R"))

options(datatable.fread.input.cmd.message=FALSE)

if(opt$num_threads < 32){

  data.table::setDTthreads(threads=opt$num_threads)

}else{

  data.table::setDTthreads(threads=32)

}

if(!is.null(opt$barcodes$barcode_sharing)){

  if(opt$barcodes$barcode_sharing == ""){

    opt$barcodes$barcode_sharing <- NULL

# 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=2.9.7

vers=2.9.7b

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-------------";