Assigned states of reference cells

[melaniebalaz]

Thank you for your work and providing this tool!
I have a question regarding the HMM prediction plots, which show the states and predicted CNV regions. These plots also show the reference cells and it looks as though they have assigned states for regions too. I was wondering how this is possible, because I thought only the observation cells would be run through the HMM and would therefore have predicted states. Moreover, if they do indeed get states assigned as well, where can I find those? Because they are not in pred_cnv_regions.dat.
I used the default analysis mode in ::run.

(Also as a related side question: To read out the states per CNV region, which files should I be reading? So far I have used

 "infercnv.17_HMM_predHMMi6.leiden.hmm_mode-subclusters.observation_groupings.txt"
"17_HMM_predHMMi6.leiden.hmm_mode-subclusters.pred_cnv_regions.dat"

because those are the furthest along the steps, where I could connect them together, however this is obviously not the last step of the model.

Thank you!