Add README file

README

+POPSIM 0.2
+
+Created by: Floreal Cabanettes
+Contact: floreal.cabanettes@inra.fr
+
+Popsim is a population CNV simulator. Generates FASTQ reads that can be used as input of a
+CNV detection workflow, like CNV detection jflow workflows suites.
+
+####################
+# How to install ? #
+####################
+
+1# Download the software from our repository using git:
+git clone --recursive git+ssh://floreal@scm.mulcyber.toulouse.inra.fr//var/lib/gforge/chroot/scmrepos/git/popsim/popsim.git
+Don't forget the "--recursive" option!
+
+2# Compile the pirs software:
+cd pirs
+make
+
+
+################
+# How to use ? #
+################
+
+Run the script build_pop.py
+
+Required parameters:
+- nb-inds: the number of individuals you want
+- reference: the reference fasta file used to build individuals
+- sv-list: a file that list of structure variants to build (see below)
+
+Optional parameters:
+- coverage: mean coverage of the reads for each individual (default: 15)
+- output-directory: directory where outputs will be written (see below) (default: <current>/res)
+- tmp-directory: temporary directory (default: <current>/tmp)
+
+
+####################################
+# How to create the SV list file ? #
+####################################
+
+This file describe the SV you want to create, and their size:
+
+DEL startLength [endLength] [increment] - Create DELetion(s).
+DUP startLength [endLength] [increment] - Create tandem DUPlication(s).
+INV startLength [endLength] [increment] - Create in-place INVersion(s).
+INR startLength [endLength] [increment] - Create INsertions from a Random source region.  Each instance has a new source.
+
+If endLength is not specified, it defaults to the value of startLength (i.e. one event will be created).
+If increment is not specified, it defaults to 1.
+
+1 line by SV type, like above.
+
+We use SVsim to generate positions of SVs. https://github.com/GregoryFaust/SVsim
+
+
+###########
+# Outputs #
+###########
+
+In the output directory there are:
+- A vcf file (genotypes.vcf) that list for each SV their position and the genotype for each individual
+- For each individual, 2 fastq files of the paired end reads (INDIV_%d_100_180_(1|2).fq.gz)
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