README for DelMapMaker

Authors: Kotaro Ishii (kotaro@riken.jp)
	 and Yusuke Kazama (ykaze@riken.jp)
Date:	22/7/2015

(1) INTRODUCTION
DelMapMaker is a Perl program for generating a CSV file representing a simulated deletion map that consists of a PCR result showing the presence or absence (a deletion) of simulated markers in simulated mutants according to user designations.

DelMapMaker generates an output file in the following manner: (a) DelMapMaker assumes a matrix that has n columns and m rows where n and m indicate the number of markers and mutants, according to user input. (b) All elements are filled with �g1,�h indicating that the marker is �gpresent.�h In each mutant, two adjacent elements in a random location are changed to �g0�h; that is, a deletion with a length of two markers is made, except when the �gbiased�h option is selected in the settings (see usage). (c) Each deletion is extended randomly from one marker to 28% of the total markers (based on the mean number in the experimental data). (d) Step (c) is repeated until the total number of �gdeleted�h (represented by �g0�h) elements equals the number input by the user. DelMapMaker outputs the virtual result as a CSV file, which can then be used as an input file for DelMapper.

DelMapper has been tested using Cygwin (version 1.7.31-3).

(2) REQUIRED SYSTEMS
-perl (an interpreter for the Perl language, see https://www.perl.org/)

(3) PACKAGE FILES
The following files are included in the DelMapMaker package.

delmapmaker.pl	# Perl script to make an input file for DelMapper
README.txt	# this file

(4) USAGE
An input file is not necessary. Instead, the numbers of virtual markers, mutants, and �gdeleted�h elements in the matrix are input by the user. 

Syntax:
   perl delmapmaker.pl [-b] nmarker nmutant ndelelement outname
where nmarker denotes the number of markers, nmutant denotes the number of mutants, and ndelelement represents the total number of �gdeleted�h elements in the matrix representing the virtual PCR result. outname is used in the names of the output directory and files.

Option:
   -b	switches on the Biased option
Usually a deletion is made in a random location (at the two adjacent markers). When the Biased option is on, this location is at the mean of the given markers, with a standard deviation of half of the number of markers.

Output file:
   outname.csv	# input file for the Perl script clusterinput.pl, which is a component of DelMapper.
The output file can be processed by clusterinput.pl without any modification.

(5) LICENSE
Copyright (c) 2015 Kotaro Ishii and Yusuke Kazama

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.