tk/Mutsel_simulator_cpg: fixed context definition

context should not include information on a codon, since it is used to
compute a rate matrix between all codons.

lib/tk/mutsel_simulator_cpg.ml

@@ -8,7 +8,6 @@ module Evolution_model = struct
   type context_CpG = {
     lh: Nucleotide.repr option;
     rh: Nucleotide.repr option;
-    codon: (Nucleotide.repr * Nucleotide.repr * Nucleotide.repr)
   }
 
   type param = {
@@ -25,12 +24,11 @@ module Evolution_model = struct
     let x, y, z = NSCodon.nucleotides codon in
     Nucleotide.(inspect x, inspect y, inspect z)
 
-  let context_CpG_of_codons p ?lh ?rh () =
+  let context_CpG_of_codons ?left_codon ?right_codon () =
     let open Option.Monad_infix in
     {
-      lh = lh >>| inspect_codon >>| trd3 ;
-      rh = rh >>| inspect_codon >>| fst3 ;
-      codon = inspect_codon p ;
+      lh = left_codon  >>| inspect_codon >>| trd3 ;
+      rh = right_codon >>| inspect_codon >>| fst3 ;
     }
 
   let fitness_of_profile ?(beta = 1.) =
@@ -43,11 +41,11 @@ module Evolution_model = struct
   let make_param ~gBGC ~scaled_fitness ~omega ~nucleotide_rates ~nucleotide_stat_dist ~rate_CpG state pos _branch =
     let context_CpG =
       if pos = 0 then
-        context_CpG_of_codons state.(pos) ~rh:state.(pos+1) ()
+        context_CpG_of_codons ~right_codon:state.(pos+1) ()
       else if pos = (Array.length state - 1 ) then
-        context_CpG_of_codons state.(pos) ~lh:state.(pos-1) ()
+        context_CpG_of_codons ~left_codon:state.(pos-1) ()
       else
-        context_CpG_of_codons state.(pos) ~lh:state.(pos -1) ~rh:state.(pos + 1) ()
+        context_CpG_of_codons ~left_codon:state.(pos -1) ~right_codon:state.(pos + 1) ()
     in
     {
       nucleotide_rates;
@@ -72,14 +70,15 @@ module Evolution_model = struct
     let scaled_fitness = Amino_acid.random_profile alpha_fitness |> fitness_of_profile in
     make_param ~gBGC:0. ~scaled_fitness ~omega:1. ~nucleotide_rates ~nucleotide_stat_dist:pi ~rate_CpG
 
-  let rate_increase_CpG (pos, x_a, x_b) context =
-    match Nucleotide.(pos, inspect x_a, inspect x_b), context with
-    | (0, C, T), { codon = (_,G, _) ; _ }
-    | (1, C, T), { codon = (_,_, G) ; _ }
-    | (2, C, T), { rh = Some G ; _ }
-    | (0, G, A), { lh = Some C ; _ }
-    | (1, G, A), { codon = (C, _, _) ; _ }
-    | (2, G, A), { codon = (_,C,_) ; _ } -> true
+  let rate_increase_CpG (pos, x_a, x_b) context codon =
+    let open Nucleotide in
+    match (pos, inspect x_a, inspect x_b), context, codon with
+    | (0, C, T), _, (_, G, _)
+    | (1, C, T), _, (_, _, G)
+    | (2, C, T), { rh = Some G ; _ }, _
+    | (0, G, A), { lh = Some C ; _ }, _
+    | (1, G, A), _, (C, _, _)
+    | (2, G, A), _, (_,C,_) -> true
     | _ -> false
 
   let fixation_probability delta =
@@ -94,7 +93,7 @@ module Evolution_model = struct
     Mutsel.NSCodon_rate_matrix.make (fun p q ->
         match NSCodon.neighbours p q with
         | Some (pos, x_a, x_b) ->
-          let rate_CpG = if rate_increase_CpG (pos, x_a, x_b) context_CpG then rate_CpG else 1. in
+          let rate_CpG = if rate_increase_CpG (pos, x_a, x_b) context_CpG (inspect_codon p) then rate_CpG else 1. in
           let _B_ = match Nucleotide.(inspect x_a, inspect x_b) with
             | (A | T), (C | G) -> gBGC
             | (C | G), (A | T) -> -. gBGC

lib/tk/mutsel_simulator_cpg.mli

@@ -6,7 +6,6 @@ module Evolution_model : sig
   type context_CpG = {
     lh: Nucleotide.repr option;
     rh: Nucleotide.repr option;
-    codon: (Nucleotide.repr * Nucleotide.repr * Nucleotide.repr)
   }
 
   type param = {