Added source code, readme and makefile

Makefile

@@ -0,0 +1,11 @@
+
+CC=g++
+CFLAGS=-lm -lz -O3 -Wall
+
+all: ngsSim
+
+ngsSim: ngsSim.cpp rbeta.cpp
+	$(CC) ngsSim.cpp -o ngsSim $(CFLAGS)
+
+clean:
+	rm -rf *o ngsSim

README.md

@@ -1,4 +1,41 @@
-ngsSim
-======
+# ngsSim
 
-NGS data simulator
+Program to simulate NGS data for up to 3 populations. It allows for variablle error rates, sequencing depth, variability, base frequencies, individual inbreeding coefficients or _Fst_. It outputs true genotypes, reads and genotype likelihoods.
+
+### Instalation
+
+To download use:
+
+    % git clone https://github.com/mfumagalli/ngsSim.git
+
+To install these tools just run:
+
+    % cd ngsSim
+    % make
+    % make test
+
+Executables are built in the main directory. If you wish to clean all binaries and intermediate files:
+
+    % make clean
+
+### Usage
+
+#### Example:
+
+    % ./ngsSim/ngsSim -outfiles pop -npop 2 -nind 20 20 -nsites 100000 -depth 4 -pvar 0.10 -F 0.3 0.3
+
+#### Parameters:
+    -outfiles: Prefix for output files
+    -npop: Number of populations. This MUST be set before -nind [1]
+    -nind: Number of diploid individuals for each population [10]
+    -nsites: Number of sites [500000]
+    -errate: The sequencing error rate [0.0075]
+    -depthMean: sequencing depth OR file with individual depths per line [5]
+    -pvar: Probability that a site is variable in the population [0.015]
+    -mfreq: Minimum population frequency [0.0005]
+    -F: FST value of 1st and 2nd split [0.4 0.1] OR inbreeding value/file in case of 1 pop [0]
+    -model: 0=fixed errate 1=variable errate (uniform distribution) [1]
+    -simpleRand: boolean [1]
+    -seed: Random number seed [0]
+    -base_freq: Background allele frequencies for A,C,G,T [0.25 0.25 0.25 0.25]
+    -expansion: Very naive method to simulate population expansion, boolean [0]