anchor.diff: -﻿namespace BioFSharp.Parallel
  +namespace BioFSharp.Parallel
   open System
   open Alea
   open Alea.FSharp
   
  -module ParallelPairwiseAlignment =
  +module PairwiseAlignment =
   
       // Conversion functions
   
       /// Character array to integer array
  -    let charsToInts (chars:char[]) =
  +    let private charsToInts (chars:char[]) =
           Array.map (fun c -> int c) chars
   
       /// Character array to string
  -    let implode (chars:char[]) =
  +    let private implode (chars:char[]) =
           chars |> System.String
   
       /// String to character array
  -    let explode (my_string:string) =
  +    let private explode (my_string:string) =
           [| for i in 0..my_string.Length-1 -> char my_string.[i] |]
   
       /// Integer array to character array. Note how I convert my -1's to hyphens.
  -    let intsToChars (ints:int[]) =
  +    let private intsToChars (ints:int[]) =
           Array.map (fun myInt -> if myInt = -1 then '-' else char myInt) ints
   
       /// String to integer array.
  -    let stringToCharInts (my_string:string) =
  +    let private stringToCharInts (my_string:string) =
           let exploded = explode my_string
           exploded |> charsToInts    
               
  
positive.code: 
      /// Primitive version of AddFloatToTrace
      [<ReflectedDefinition>]
      let AddFloatToTrace (ts:TraceScore) (opc:int) =
          ts.Value + opc
  
      /// Primitive version of DiagonalCost
      [<ReflectedDefinition>]
      let diagonalCost (cell:Cell) (item1:int) (item2:int) =
          let sim' = if item1 = item2 then 5 else -4
          let mM = AddFloatToTrace cell.M sim' 
          let mY = AddFloatToTrace cell.Y sim' 
  
negative.code:         i_best, j_best
  
      /// Primitive version of TraceBackZerovalue. Note how I represent a gap with a "-1"
      let rec private traceBackPrimitive (fstSeq:int[]) (sndSeq:int[]) (i:int) (j:int) (acc1:int list) (acc2:int list) (matrix:Cell[,]) =
          match matrix.[i,j].M.TraceType with
          |0uy -> acc1, acc2
          |1uy -> traceBackPrimitive fstSeq sndSeq (i-1) (j-1) (fstSeq.[i-1]::acc1) (sndSeq.[j-1]::acc2) matrix
  