odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
61 stars 9 forks source link

Avg phaseQ value in usage document #27

Closed koido closed 1 year ago

koido commented 1 year ago

Hi Olivier,

I found a potential inconsistency between the Avg phaseQ value in the usage and the actual values observed in the logs.

The Documentation states, "We usually expect values above 0.8 or even 0.9." However, I noticed that my actual log values are much larger (over 90).

Upon examining the code, the phaseQ calculation appears to produce values in the range of 0 to 99.

I suspect the description of the phaseQ value range might be "above 80 or even 90" instead of "0.8 or even 0.9." Is my interpretation correct?

I'm using v5.1.0.

Many thanks again.

Best, Masaru

odelaneau commented 1 year ago

Thanks for spotting this. I updated the documentation accordingly.

koido commented 1 year ago

Many thanks for the update!