--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/rdiff.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,78 @@
+function []=rdiff(ARGS)
+% rdiff()
+%
+
+if isempty(ARGS)
+    usage() ;
+    exit(-1) ;
+end
+%ARGS=[ARGS ':.:.'] ;
+
+%%% Add paths  %%%
+fprintf('Set the paths\n')
+CFG.paths = set_rdiff_paths();
+
+
+%%% Read configuration file %%%
+fprintf('Load configuration\n')
+CFG = configure_rdiff(CFG);
+CFG = process_command_line_args(CFG,ARGS);
+CFG = process_configure_rdiff(CFG);
+
+%%% Get read counts %%%
+
+%load the gene structure
+load(CFG.genes_path , 'genes');
+
+% mask the regions which overlap with other genes
+fprintf('Compute regions common to multiple genes\n')
+[genes]=detect_overlapping_regions(genes);
+
+%Precompute testing regions
+fprintf('Compute alternative regions\n')
+[genes]=compute_testing_region(CFG,genes);
+
+%Get the gene expression
+if CFG.estimate_gene_expression
+    fprintf('Measure gene expression\n')
+    get_read_counts(CFG,genes);
+end
+
+%%% Estimate variance function %%%
+if CFG.perform_nonparametric
+    variance_function_nonparametric_1=[];
+    variance_function_nonparametric_2=[];
+    [variance_function_nonparametric_1, variance_function_nonparametric_2]=estimate_variance_nonparametric(CFG,genes);
+end
+
+if CFG.perform_poisson
+    variance_function_parametric_1=[];
+    variance_function_parametric_2=[];
+end
+if CFG.perform_parametric
+    variance_function_parametric_1=[];
+    variance_function_parametric_2=[];
+    [variance_function_parametric_1, variance_function_parametric_2]=estimate_variance_parametric(CFG,genes); 
+end
+
+%If only gene expression is needed, stop here
+if CFG.only_gene_expression
+    return
+end
+
+
+%%% Perform tests &  Write output %%%
+
+%Run the prametric tests
+if or(CFG.perform_parametric,CFG.perform_poisson)
+    perform_parametric_tests(CFG,genes,variance_function_parametric_1, variance_function_parametric_2)
+end
+%Run the nonparametric tests
+if or(CFG.perform_nonparametric,CFG.perform_mmd)
+    perform_nonparametric_tests(CFG,genes,variance_function_nonparametric_1, variance_function_nonparametric_2)
+end
+
+return
+
+
+