anchor.diff:              //Usage: hmmsearch [options] <hmmfile> <seqdb>
   
           let runHMMsearchAsync (bcContext:BioContainer.BcContext) (opt:HMMsearchParams list) = 
  -            //Usage: hmmbuild [-options] <hmmfile_out> <msafile> -> filter for in/out and move them to the end
  +            //hmmsearch [options] hmmfile seqdb
               let hmm     = 
                   opt 
                   |> List.filter (fun p -> match p with |InputHMMFile _ -> true |_ -> false)
  
positive.code:                     return res
   
              }
          ///Perform a multiple sequence alignment of all the sequences in seqfile by aligning
          ///them individually to the profile HMM in hmmfile. The new alignment is output to
          ///stdout.
          let runHMMalign (bcContext:BioContainer.BcContext) (opt:HMMsearchParams list) =
              runHMMsearchAsync bcContext opt
              |> Async.RunSynchronously
  
negative.code: 
              let options = opt |> List.filter (fun p -> match p with |InputHMMFile _ |SequenceDB _ -> false |_ -> true)
              let cmds = (options |> List.map (HMMsearchParams.makeCmdWith bcContext.Mount))
              let tp = ("hmmsearch"::(cmds |> List.concat))@hmm@seqDB
  
              printfn "Starting process hmmsearch\r\nparameters:"
              printfn "%s" hmm.[0]
              printfn "%s" seqDB.[0]
              cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op))
  