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{ 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 *) {This manual page was created by makman 1.45}{created by htmlink 1.62}