added lethal mutations

stdpopsim/catalog/HomSap/dfes.py

@@ -1,4 +1,4 @@
-import math
+caimport math
 import stdpopsim
 
 _species = stdpopsim.get_species("HomSap")
@@ -150,7 +150,7 @@ def _HuberLogNormalDFE():
 
 
 def _KyriazisDFE():
-    id = "GammaPlus_K23" # *** is Gamma specific enough?
+    id = "Mixed_K23"
     description = "Deleterious Gamma DFE with additional lethals"
     long_description = """
     Return neutral and negative MutationType()s representing a human DFE.
@@ -174,17 +174,19 @@ def _KyriazisDFE():
     gamma_mean = 0.0131
     gamma_shape = 0.186
     coeffs = [0.45,  0.2,  0.05, 0]
-    breaks = [0.001, 0.01, 0.1, 1]
+    breaks = [0.001, 0.01, 0.1]
     gamma = stdpopsim.MutationType(
         dominance_coeff_list = coefs,
         dominance_coeff_breaks = breaks,
         distribution_type="g",  # gamma distribution
         distribution_args=[gamma_mean, gamma_shape],
     )
+    h=0
+    s=1
     lethal = stdpopsim.MutationType(
-        dominance_coeff_list = coefs,
-        dominance_coeff_breaks = breaks,
-        <<selection_coeff???>> = 1      ## *******
+        distribution_type="f", # fixed value
+        distribution_args=[-1],
+        dominance_coeff=h,
     )    
     # To get 0.63 deleterious mutations per 30Mb diploid coding sequence with 
     # mu=1.29e-8 (current mu from catalog), we need a deleterious proportion