Alistat.nucleotide_fasta_gc: compute GC stats at any pos in codon

lib/alistats.ml

@@ -5,9 +5,9 @@ let ok_exn err = function
   | Ok x -> x
   | Error e -> failwith (err e)
 
-let is_gc ?thirdpos:(tp=false) i c =
-  match tp with
-  | true when not ((i mod 3) = 2) -> false
+let is_gc ?pos i c =
+  match pos with
+  | Some p when not ((i mod 3) = p) -> false
   | _ -> c = 'g' || c = 'G' || c = 'c' || c = 'C'
 
 let strings_from_fasta fa =
@@ -21,11 +21,17 @@ type gc_stat = {
   gc_variance_among_sequences : float ;
 }
 
-let nucleotide_fasta_gc ?thirdpos:(tp=false) fa =
+let nucleotide_fasta_gc ?pos fa =
+  let pos = Option.map pos ~f:(function
+      | `first -> 0
+      | `second -> 1
+      | `third -> 2
+    )
+  in
   let seqs = strings_from_fasta fa in
   let gc_counts = Array.map seqs ~f:(fun seq ->
-      let len = if tp then String.length seq / 3 else String.length seq in
-      let sum = String.foldi ~init:0 ~f:(fun i a c -> a + if is_gc ~thirdpos:tp i c then 1 else 0) seq in
+      let len = if pos <> None then String.length seq / 3 else String.length seq in
+      let sum = String.foldi ~init:0 ~f:(fun i a c -> a + if is_gc ?pos i c then 1 else 0) seq in
       float len, float sum
     )
   in