Delila Program: range

range program

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

{version = 1.03; (* of range.p 1997 April 22}

(* begin module describe.range *)
      range: determine the range of bases in the inst/book

      range(inst: in, book: in,
            output: out)

      inst: delila instructions of the form 'get from 56 -5 to 56 +10;'
         If this file is empty, then the sequences will be
         aligned either by their 5' ends or by their zero base,
         depending on the 4th parameter in rangep.

      book: the book generated by delila using inst

      rangep: parameters to control the program.  There is only one
         parameter, the method of alignment.  See alist for further details.

         If the first character is
         'f' (for 'first') then the sequences are always aligned by their
         first base.

         'i' then the sequences are aligned by the delila instructions.  If
         the inst file is empty, alignment is forced to the 'b' mode.

         'b' (for 'internal') then the alignment is on the internal zero of
         the book's sequence.  This option is to be used when "default
         coordinate zero" is used in the Delila instructions.

      therange: Three lines:
         two integers on one line giving the range: from and to.
         just the from
         just the to

      output: messages to the user


      The range program determines the range of the book as aligned by inst.
      By giving the range in two forms (on one line and separate)
      external programs can easily obtain the required data.



see also

      Thomas D. Schneider


technical notes

(* end module describe.range *)
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