samtools path

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

## Changelog

18 Sept 2020: zUMIs.2.9.4b/c/d: Fix & speed up Smart-seq3 UMI read counting. Prevent crash when a chunk of cell BCs does not match any downsampling. Speed up barcode detection steps for some cases. Prevent too much CPU usage in UMI error correction.

18 Sept 2020: zUMIs.2.9.4b/c/d/e: Fix & speed up Smart-seq3 UMI read counting. Prevent crash when a chunk of cell BCs does not match any downsampling. Speed up barcode detection steps for some cases. Prevent too much CPU usage in UMI error correction. Take correct samtools executable in gene annotation parsing.

12 Sept 2020: [zUMIs2.9.4](https://github.com/sdparekh/zUMIs/releases/tag/2.9.4): Speed writing of error-corrected UMI tags to bam file up significantly. Prevent potential crash when no cells meet any user-defined downsampling criteria.

# }

# reads information from Bam file on lengths and names of chromosomes/scaffolds. Can exclude scaffolds based on their size if desired.

.chromLengthFilter <- function(abamfile, keep_chr_minLength =0){

  bread<- paste("samtools view -H ", abamfile , "| grep '^@SQ' | cut -f2,3 ")

.chromLengthFilter <- function(abamfile, keep_chr_minLength =0, samtoolsexc){

  bread<- paste(samtoolsexc,"view -H ", abamfile , "| grep '^@SQ' | cut -f2,3 ")

  chr<-data.table::fread(bread,col.names = c("chr","len"), header = F)[

                              , chr2 :=gsub("SN:","",chr)][ 

                              , len2 :=gsub("LN:","",len)][

}

#new version of makeSAF by Chris Alford

.makeSAF<-function(gtf, extension_var=FALSE, exon_extension=0, buffer_length=100, scaff_length=0,multi_overlap_var=FALSE){

.makeSAF<-function(gtf, extension_var=FALSE, exon_extension=0, buffer_length=100, scaff_length=0,multi_overlap_var=FALSE, samtoolsexc){

  print("Loading reference annotation from:")

  print(gtf)

  gtf_file <- plyranges::read_gff(gtf, col_names = c("type","gene_id"))

  #Calculating total intergenic length for intron-probability

  totalGeneLength<-sum(width(gr.gene))

  #get length of chromosomes from BAM header

  chrL<-system( paste("samtools view -H", abamfile ," | grep '^@SQ' | cut -f3 "), intern = T)

  chrL<-system( paste(samtoolsexc,"view -H", abamfile ," | grep '^@SQ' | cut -f3 "), intern = T)

  chrL<-lapply(chrL, function(x){

    x<-as.integer(strsplit(x, ":")[[1]][[2]])

  })

  intergenicBp<- chrL-totalGeneLength

  # getting names and length of chromosomes/scaffolds from bam header

  chrom_kept <- .chromLengthFilter(abamfile = abamfile, keep_chr_minLength = scaff_length)

  chrom_kept <- .chromLengthFilter(abamfile = abamfile, keep_chr_minLength = scaff_length, samtoolsexc = samtoolsexc)

  # reading out chromosomes/scaffold names from the GRange gtf object

  chrom_gtf_names <- tibble::as_tibble(x = list("chrom_names" = as.character(seqinfo(gtf_file)@seqnames)),

              exon_extension = opt$reference$extension_length,

              buffer_length = (opt$reference$extension_length / 2),

              scaff_length = opt$reference$scaffold_length_min,

              multi_overlap_var = opt$counting_opts$multi_overlap)

              multi_overlap_var = opt$counting_opts$multi_overlap,

              samtoolsexc = samtoolsexc)

try(gene_name_mapping <- .get_gene_names(gtf = paste0(opt$out_dir,"/",opt$project,".final_annot.gtf"), threads = opt$num_threads), silent = TRUE)

try(data.table::fwrite(gene_name_mapping, file = paste0(opt$out_dir,"/zUMIs_output/expression/",opt$project,".gene_names.txt"), sep ="\t", quote = FALSE), silent = TRUE)

##

# 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=2.9.4d

vers=2.9.4e

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