Similar to #9 I have a question regarding the interpretation of scores and comparments. As you mention in the issue, a positive or negative value is assigned randomly as it makes no difference to the likelihood function if it sees ABAB or BABA. Does this hold both for samples and individual chromosomes? So do I need to define for each chromosome in each sample separately the positive or negative sign of the A and B compartments?
(Edit: probably yes, as #3 also has a similar issue.)
Similar to #9 I have a question regarding the interpretation of scores and comparments. As you mention in the issue, a positive or negative value is assigned randomly as it makes no difference to the likelihood function if it sees ABAB or BABA. Does this hold both for samples and individual chromosomes? So do I need to define for each chromosome in each sample separately the positive or negative sign of the A and B compartments?
(Edit: probably yes, as #3 also has a similar issue.)