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Add alternative allele probability input and MetaFounder support
Conditional statement added to remove error "NoneType object is not subscriptable".
Testing for an edge case with metafounders
Minor correction to allow the input of the alternative allele frequency by the user. This is now working!
Implementation of an error message if the user inputs a main_metafounder that does not start with "MF_".
Update to conditional statement for founders
Changed integer to a float to allow decimal place on input e.g 0.5, 0.45 etc. Previously was forced on input to be an integer (then later turned into a float).
Allow AAP to be non-integer
Implementation details for metafounders were added through comments in pedigree.py.
Coding Comments on Metafounder Implementation
Metafounders
-Update segregation prob and error matrix for x chromsome -Update log -Change all to XChrMaleFlag
Corrected formatting for X chromosome's generateSegregation and errorMatrix entry.
Removed .copy()
Inclusion of phenotype information
X chromosome functionality
Code to handle two different metafounders assigned to an individual.
Updating error messages and metafounder rules thanks to @RosCraddock! We can address the required flexibility for two diff MF for two founders later.
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