The default format for the CSV files in a R/qtl2 bundle is:

matrix of individuals × (markers/phenotypes/covariates/phenotype covariates/etc.)

(A) (f/F)ile(s) in the R/qtl2 bundle could however

• be transposed,

which means the system needs to "un-transpose" the file(s) before processing.

Currently, the system does this by reading all the files of a particular type, and then "un-transposing" the entire thing. This leads to a very slow system.

This issue proposes to do the quality control/assurance processing on each file in isolation, where possible - this will allow parallelisation/multiprocessing of the QC checks.

The main considerations that need to be handled are as follows:

• Do QC on (founder) genotype files (when present) before any of the other files
• Genetic and physical maps (if present) can have QC run on them after the genotype files
• Do QC on phenotype files (when present) after genotype files but before any other files
• Covariate and phenotype covariate files come after the phenotype files
• Cross information files … ?
• Sex information files … ?

We should probably detail the type of QC checks done for each type of file