Summary of TODO tasks in AlphaGenes/AlphaPeel#219 discussion

[XingerTang]

• Round up threshold for output file names (link)
• Update help messages in documentation in accordance with the change in Polish of the usage and TODOs to clarify and simplify options #219 (link)
• Rename mutation_rate to mut_prob (link)
• Add explanation of no_phase_founder to documentation (link)
• Remove no_param and modify the relevant output logic (link)
• Design tests for all parameters, covered in Revise tests #67 (link)
• Change estimation limits of base population allele frequency from [0.01, 0.99] to something wider #185 (link)
• Add sequence input option for X chr (link)
• Add explanation of rec_length in documentation (link)
• Add example of seg_map_file in documentation (link)
• Change the file format of genotype probabilities file? #117 (link)
• Add visual aids for the explanation of segregation probabilities in documentation (link)

Next step:

• Prioritise the tasks
• Create relevant task issues and assign the tasks