Commit 3ef70087 authored by ziegenhain@bio.lmu.de's avatar ziegenhain@bio.lmu.de
Browse files

fix stats feature plot

parent 7b3969bb

UMIstuffFUN.R

+1 −1
Original line number Diff line number Diff line
@@ -48,7 +48,7 @@ reads2genes <- function(featfiles,chunks,rgfile,cores){ 
  ## minifunction for string operations

  nfiles=length(featfiles)

  write.table(file=rgfile,chunks,col.names = F,quote = F,row.names = F)

  headerXX<-paste( c(paste0("V",1:14)) ,collapse="\t")

  headerXX<-paste( c(paste0("V",1:3)) ,collapse="\t")

  write(headerXX,"freadHeader")

  samcommand<-paste("cat freadHeader; samtools view -x NH -x AS -x nM -x HI -x IH -x NM -x uT -x MD -x jM -x jI -x XN -x XS -R",rgfile,"-@",cores)

statsFUN.R

+3 −3
Original line number Diff line number Diff line
@@ -7,12 +7,12 @@ sumstatBAM <- function(featfiles,cores,outdir,user_seq,bc,outfile){ 
  require(data.table)

  # check for user defined sequences

  ## minifunction for string operations

  headerXX<-paste( c(paste0("V",1:14)) ,collapse="\t")

  headerXX<-paste( c(paste0("V",1:3)) ,collapse="\t")

  write(headerXX,paste(outdir,"freadHeader",sep="/"))

  samcommand<-paste("cat freadHeader; samtools view -x NH -x AS -x nM -x HI -x IH -x NM -x uT -x MD -x jM -x jI -x XN -x UB -@",cores)

  #issue with BC matching

  mapCount<-data.table::fread(paste(samcommand,featfiles[1],"| cut -f12,13,14 | sed 's/RG:Z://' | sed 's/UB:Z://' | sed 's/XT:Z://' "), na.strings=c(""),

                             select=c(1,2,3),header=T,fill=T,colClasses = "character" , col.names = c("RG","UB","GE") )[

  mapCount<-data.table::fread(paste(samcommand,featfiles[1],"| cut -f12,13,14 | sed 's/RG:Z://' | sed 's/XS:Z://' | sed 's/XT:Z://' "), na.strings=c(""),

                             select=c(1,2,3),header=T,fill=T,colClasses = "character" , col.names = c("RG","XS","GE") )[

                              ,"GEin":=fread(paste(samcommand,featfiles[2],"| cut -f13,14 | sed 's/XT:Z://'"),select=2,header=T,fill=T,na.strings=c(""),colClasses = "character")

                               ][ ,"ftype":="NA"

                               ][is.na(GEin)==F,ftype:="Intron"

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