add tumor_id and normal_id for run-facets-wrapper.R

[stevekm]

The run-facets-wrapper.R script requires tumor-normal output from snp-pileup. However, the script does not seem to offer any way to record the ID for the tumor and normal samples. It has an arg for --sample-id which says "preferrable Tumor_Normal to keep track of the normal used". But this does not work when your sample ID's contain _ characters. So, based on the current sample_id value that is used, there's no actual way to distinguish between the original tumor_id and the normal_id used.

It looks like there are several places where the sample_id is added to output files with this function;

add_column(sample = sample_id, .before = 1)

Can we just add some extra command line args for tumor_id and normal_id and use the same function to add those to the output as well?

Example;

...
parser$add_argument('--tumor-id', required = FALSE,
                    help = 'Tumor ID, to keep track of tumor sample used')
parser$add_argument('--normal-id', required = FALSE,
                    help = 'Normal ID, to keep track of the normal sample used')

...
add_column(tumor = tumor_id, .before = 1)
add_column(normal = normal_id, .before = 1)