Delila Program: malin

malin program

Documentation for the malin program is below, with links to related programs in the "see also" section.

{   version = 1.14; (* of malin.p 2009 Apr 11}

(* begin module describe.malin *)
(*
name
   malin: make delila instructions from nth alignment of malign

synopsis
   malin(optinst: in, optalign: in, inst: in, malinp: in,
         cinst: out, distribution: out, output: out)

files
   optinst: output of malign program containing absolute alignments

   optalign: output of malign program containing relative alignments

   inst: Delila instructions
      Allowed forms:

       get from 5 -5 to 5 +5;
       get from 5 -5 to same +5;
       get from 5 -5 to piece end -5;

   malinp: parameters to control the program
      first line: The version number of the program.  This allows the user to
         be warned if an old parameter file is used.

      second line:  one integer that defines which alignment to use
         to create the cinst.

      third line:  one integer that defines how much to add to
         move the location of the zero base in the new instructions.

   cinst: Delila instructions of inst converted to the alignment
      of optinst chosen in malinp

   distribution: The distribution of the realignment.  Lines that begin with
      "*" are comments.  Otherwise, one integer per line, which is the
      separation in bases between the initial and final alignments.

   output: output program without private text

description
   This program allows one to select one of the alignments created by malign
   and to make the corresponding Delila instructions.  Because it copies the
   inst file it keeps the organism and chromosome information (along with all
   comments) so it is better than the "bestinst" file created by malign!

examples

documentation

see also

   example parameter file: malinp
   related programs: malign.p, malopt.p

author
   Thomas Dana Schneider

bugs
   WARNING:  This program does not use a book and so the coordinate
   shift of the third parameter will not work on coordinates that jump.

technical notes

   NOTE: THIS PROGRAM WILL NOT HANDLE COMMENTS WITHIN THE DELILA
   INSTRUCTION!  It must be of the form:
      get from 193 -20 to 193 +21;
   comments are allowed outside these statements.

*)
(* end module describe.malin *)
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