--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/get_nonparametric_tests_caller.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,109 @@
+function []=get_nonparametric_tests_caller(PAR)
+
+
+CFG = PAR.CFG;
+genes = PAR.genes;
+OUT_STR='';
+
+% add paths
+addpath(CFG.paths);
+%load local variables
+data_dir=CFG.data_dir;
+OUT_STR=[];
+
+variance_function_nonparametric_1=PAR.variance_function_nonparametric_1;
+variance_function_nonparametric_2=PAR.variance_function_nonparametric_2;
+
+Counts_rDiff_nonparametric=PAR.Counts_rDiff_nonparametric;
+Gene_expression=PAR.Gene_expression;
+
+%clear variabe PAR
+clear PAR;
+
+NUMBER_OF_TESTS_PER_GENE=(CFG.perform_nonparametric+CFG.perform_mmd);
+if NUMBER_OF_TESTS_PER_GENE==0
+    return
+end
+P_VALS=cell(size(genes,2),NUMBER_OF_TESTS_PER_GENE+2);
+
+
+%iterate over genes
+for i=1:size(genes,2)
+    
+    %TEMP_COUNT contains the counts for the current gene
+    TEMP_COUNT=cell(1,3);
+    gene = genes(i);
+    
+    
+    OLD_OUT_STR=OUT_STR;
+    OUT_STR=['Current gene: ' gene.name ];
+    %print progress
+    if CFG.use_rproc
+        fprintf([OUT_STR '\n'])
+    else
+        % Erase old progress
+        fprintf(repmat('\b',1,length(OLD_OUT_STR)));
+        fprintf([OUT_STR])
+    end
+    
+    %set default return values
+    P_VALS{i,1}=gene.name;
+    
+    %check that the gene has exons defined
+    if isempty(gene.exons)
+        P_VALS{i,4}='Exons field empty in gene structure';
+        continue;
+    end
+    
+    %check that the gene is longer than the Reads. Otherwise the
+    %definition of regions does not makes sense
+    if gene.stop-gene.start<CFG.sequenced_length+3
+        continue;
+    end
+    %perform 
+    
+    
+    %Get the reads
+    READ_SET={};
+    for bam_ix=1:length(CFG.BAM_FILES)
+        CFG.curr_bamfile=CFG.BAM_FILES{bam_ix};
+        READ_SET{end+1} = get_reads_for_gene(CFG,gene);
+    end
+    %merge the reads per sample
+    SAMPLE1=find(CFG.SAMPLES==1);
+    SAMPLE2=find(CFG.SAMPLES==2);
+    
+       
+    COUNTER=2;
+    
+    if CFG.perform_mmd
+        reads1=[];
+        reads2=[];
+        SAMPLE_LENGTH1=length(SAMPLE1);
+        SAMPLE_LENGTH2=length(SAMPLE2);
+        for bam_ix=1:SAMPLE_LENGTH1
+            reads1=[reads1;READ_SET{SAMPLE1(bam_ix)}];
+        end
+        
+        for bam_ix=1:SAMPLE_LENGTH2
+            reads2=[reads2;READ_SET{SAMPLE2(bam_ix)}];
+        end
+        [PV, INFO]= rDiff_mmd(CFG,reads1,reads2);
+        P_VALS{i,COUNTER}={PV, INFO};
+        clear reads1
+        clear reads2
+        COUNTER=COUNTER+1;
+    end
+    
+    if CFG.perform_nonparametric
+        [PV, INFO]= rDiff_nonparametric(CFG,READ_SET(SAMPLE1),READ_SET(SAMPLE2),variance_function_nonparametric_1, variance_function_nonparametric_2);
+        P_VALS{i,COUNTER}={PV, INFO};
+        COUNTER=COUNTER+1;
+    end
+    
+end
+fprintf('\n')
+%Save the p-values
+OUT_FILENAME=[CFG.outfile_prefix '.mat'];
+save(OUT_FILENAME,'P_VALS')
+