ReadMGATK does not work if using -eb option in mgatk

[msteph11]

Hello,

When using the -eb option in mgatk (which adds columns for base quality scores in the A,G,T,C matrices) the resulting output folder cannot be read using the ReadMGATK function. Below is the error given:

> test <- ReadMGATK(path)
Reading allele counts
Error in read.table(file = a.path, sep = ",", header = FALSE, stringsAsFactors = FALSE,  : 
  more columns than column names

If the extra columns are removed from the matrices, the folder can be read using the ReadMGATK function, but calling IdentifyVariants causes RStudio to unexpectedly crash while processing C.

> vars <- IdentifyVariants(test$counts, test$refallele)
Computing total coverage per base
Processing A
Processing T
Processing C

[timoast]

Do you have an example output with the --eb option set that I could take a look at? You can email a download link to stuartt@gis.a-star.edu.sg