call_phase argument not documented

[janaobsteter]

From the documentation it is unclear how to get phased genotyped from the input.

1. The call_phase argument is not documented - I see it in the example code, but not in the manual. It is also not completely clear to me whether I need both, -calling_threshold and -call_phase
   

2. It would be good to mention here in the outputs that the phase file is only produced, if the user specifies the -calling_threshold and -call_phase (I think it would help with the understanding)
   

[gregorgorjanc]

@janaobsteter we (@XingerTang and @AprilYUZhang) are well aware of how these docs are unclear and we are working on a rewamp of the docs as well as more functionality in this space. See all the options opened and also work going on at https://github.com/AlphaGenes/AlphaPeel/tree/devel/docs

[gregorgorjanc]

@janaobsteter could you work with the devel version and report what is not clear in that version?