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{version = 1.08; (* of gap.p 1993 Jan 26} (* begin module describe.gap *) (* name gap: gaps in aligned listing of a book synopsis gap(inst: in, book: in, gapp: in, data: out, output: out) files 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 number. 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 description 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. example documentation see also alist.p author Thomas D. Schneider bugs as in alist.p technical notes *) (* end module describe.gap *) {This manual page was created by makman 1.45}{created by htmlink 1.62}