[GEN-562] Cross-validate maf with clinical sample files

[rxu17]

Purpose: This PR adds further cross-validation functionality by adding the ability to cross-validate ids in the maf files with the clinical sample files.

This uses the newly introduced ancillary_files attribute in the specific filetypeformat classes to cross validate.

[thomasyu888]

This is a wonderful start, let's discuss more soon

[rxu17]

@thomasyu888 I updated the structure so this is what the cross validation will generally look like for other cross validation tickets we use. Let me know what you think (I can also move cross_validate_ids_between_two_files to the validate class), and I'll move forward with this.

• Copy the get_dataframe from the individual filetypeformat class to process_functions and rename it as specific to the filetypeformat class it belongs to
• Each filetypeformat class's _cross_validate function will loop through ancillary_files (which is just the result of extract.get_center_files now) and get the file that we are trying to cross validate against so we can read it in
• Do specific cross-validation specific to the filetypeformat object pair

When we do change the structure of get_center_files/separate out the clinical files, we should be able to just modify each filetypeformat class's _cross_validate function and remove the places that loop through the list of lists as well as just removing the get_dataframe function we copied to process_functions and replace it with the class specific one. Everything else should stay the same.

I might just make the section of the code where we loop through the ancillary_files as its own function so easier to remove in the future.