Command line interface improvements:
- Help/usage text is better formatted and more descriptive
- Values provided for optional arguments are checked to ensure they are the correct type and within an expected range
- New optional arguments to specify molarity of primers and probes
Report improvements:
- Better formatting for oligo site seqs in PCR_results and oligo site variants in variant_report: lower case bases for mismatches, base in parentheses for insertions, and dashes for deletions
Error handling:
- Checks that input assay CSV file and genomes FASTA file exist and are not empty
- Checks that output directory exists
- Checks that oligo seqs provided in assay CSV file contain only recognized IUPAC nucleotide codes
- Fixed bug raising key value errors when missed_seqs_report data frame was empty