Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

[Nicklas Nordborg]

In 7324:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Added a --debug option to the run_ascat.R script that save the ascat.bc and ascat.output objects to .Rdata files. This will be useful for manual inspection and testing without having to re-run everything before every time.

[Nicklas Nordborg]

In 7325:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Saving the NonAberrant flag to the stats.txt file. It is outputted as a 0/1 value.

[Nicklas Nordborg]

In 7326:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Created the NonAberrant annotation type. It can have values "Yes" or "No", but we only set the "Yes" value if the flag is present in the ASCAT output.

[Nicklas Nordborg]

In 7327:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Display the "Non-aberrant" flag in the confirmation wizard and case summary.