Refactor minor fixes

[XingerTang]

What changed

• Description of method option
• Description of alt_allele_prob option
• Description of genotype probabilities

Why this change

• method does not have a default value while parsing the arguments, but if there is no input for the option, then the program would run in the multi mode. We can see it as equivalent to having a default value of multi.
• alt_allele_prob won't give posterior alternative allele probabilities; other options that prompt outputs either give the posterior probabilities, such as seg_prob, hap, or will warn the user during the run, such as pheno_penetrance_prob. Therefore, it is worth noting.
• Update genotype probabilities format description for sex chromosome for males.

Notes / Risks

• Minor changes only

[gregorgorjanc]

This won’t be clear to most as it’s too cryptic.

I suggest the following.

1. Take the X example input from the above (there id1 and id3 are males…)
2. Get genotype probabilities for the example
3. Create a separate output example for the X chromosome below the autosomal chromosome
4. Add this text above that example
5. Mention that for females the interpretation is as for an autosomal chromosome below, but for males …

I will then suggest edits

[gregorgorjanc]

@XingerTang nice that you are polishing these bits! Great! I have suggested some improvements for documenting X chr genotype probability output

[gregorgorjanc]

Suggested change

	When working with the X chromosome, for female individual, the interpretation
	When working with the X chromosome, for a female individual, the interpretation

[gregorgorjanc]

Suggested change

	is as for an autosomal chromosome above. For male individual, the first line and
	is as for an autosomal chromosome above. For a male individual, the first line and

[gregorgorjanc]

Suggested change

	the last line corresponding to ``a`` and ``A`` respectively, with the middle
	the last line respectively correspond to ``a`` and ``A`` genotypes, with the middle

[gregorgorjanc]

Apply the same edits as above

[gregorgorjanc]

Minor edits and we merge this in

[gregorgorjanc]

Merge-away @XingerTang ;) Yay.

[gregorgorjanc]

Aha, I assume you squash and merge.

[XingerTang]

Great. Squash done.