Delila Program: gap

gap program

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

{version = 1.08; (* of gap.p 1993 Jan 26}

(* begin module *)
      gap: gaps in aligned listing of a book

      gap(inst: in, book: in, gapp: in, data: out, output: out)

      inst: delila instructions of the form 'get from 56 -5 to 56 +10;'
         (This file may be empty, in which case the sequences will be
         aligned by their 5' ends.)
      book: the book generated by delila using inst
      gapp: parameters to control the program.  If empty, the range of the
         instructions are used.  Otherwise,
         1. The first line contains one line with two integers
         defining the range to find gaps in.  This allows one to have a wide
         alignment, but look only at a portion.  (This is equivalent to the
         alist display range.)
  2. If the first character of the second line is 'p' the piece
  information is given in the data list.
         3. minimum number of gaps to report
         4. modulus: integer. Gaps are reported if if (gap mod modulus) = 0.
            For example, if modulus = 5, only gaps of 5 long are reported.
            To get all gaps, use modulus = 1.
      data: the gap listing.  First column is the number of gaps.
  If the sequences are numbered, the second column is the sequence
         If the display is on (2nd parameter), then the piece name is given,
         followed by the coordinate of the zero base.
      output: messages to the user

      Gap is useful for determining the distribution of gaps in an aligned set.
      The pieces in the book are aligned according to the instructions in
      file inst, and listed in the list file.  Each piece is identified.



see also

      Thomas D. Schneider

   as in alist.p

technical notes

(* end module *)
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