[GEN-973] Fix bed file-clinical file cross-validation

[rxu17]

Purpose: This is to add a fix to the cross validation for bed files against SEQ_ASSAY_IDs in clinical files

Changes: Changes were added to _cross_validate_bed_files_exist to do the following:

• Split the original function into one that outputs the missing bed files and one that outputs errors/warnings for ease of testing
• Standardizes the SEQ_ASSAY_IDs first then get a unique list of them to loop through

Testing:

• Tests were modified to have different case/underscored SEQ_ASSAY_ID values in the clinical file