paired analysis - samples with NULL replicates

[josegarciamanteiga]

Hi, I have encountered the following error: "Error in psiFirst[[lstInd]] : subscript out of bounds"

While debugging I see that for my first mclapply round (i=1)

psiFirst [[1]] NULL

[[2]] NULL

[[3]] NULL

psiSecond [[1]] NULL

[[2]] NULL

[[3]] NULL

I have a problem with this lines:

  # if(opt$paired) { #make sure both samples have a non-NULL replicate
  #   for(lstInd in 1:length(psiFirst)) {
  #     if(is.null(psiFirst[[lstInd]]) || is.null(psiSecond[[lstInd]])) {
  #       psiFirst[[lstInd]] <- NULL
  #       psiSecond[[lstInd]] <- NULL
  #     }
  #   }
  # }

The first line of the input file (.tab) produces NULL replicates since the total reads do not pass the filters, the script should just go Next, if I understood it correctly, but this checking loop produces an error since every time it applies <-NULL it reduces the dimension and it produces the error in my case at the last replicate. I have commented the lines and launched it interactively and the error is not there anymore. Could you please confirm it? Thank you