Develop menu for CLI

[hyphaltip]

Need to develop the menus for relocate3.py to run the steps. Reminder the goal is to run the mapping/aln step of each strain/individual as a separate independent job, produce summary results (BAM?, BED?) files of the reads which contain TEs and their locations in the reference genome.

Proposed menu function names could be

• process_individual -- eg map reads for an individual to a genome (1-N seq libraries)
• gather_mapped_individual -- eg gather the mapped read locations to score the TE
• statistics
• classify -- eg classify reference and non-reference insertions, homozygous/heterozygous