--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/get_read_counts.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,158 @@
+function []=get_read_counts(CFG,genes)
+
+if CFG.use_rproc
+   JB_NR=1;
+   JOB_INFO = rproc_empty();
+end
+
+%%% Get the read counts
+if CFG.estimate_gene_expression==1
+    for RUN=1:size(CFG.BAM_FILES,2)
+        % configuration
+        CFG.curr_bamfile = CFG.BAM_FILES{RUN};
+        if not(CFG.use_rproc)
+            fprintf('Getting gene expression for: %s\n', CFG.curr_bamfile);
+        end
+        tic
+        %define the splits of the genes for the jobs
+        idx=[(1:size(genes,2))',ceil((1:size(genes,2))*CFG.rproc_num_jobs/size(genes,2))']; 
+        % submit jobs to cluster
+        for i = 1:CFG.rproc_num_jobs
+            PAR.genes = genes(idx(idx(:,2)==i,1)); 
+            CFG.rproc_memreq = 5000;
+            CFG.rproc_par.mem_req_resubmit = [10000 20000 32000];
+            CFG.rproc_par.identifier = sprintf('Exp.%i-',i);  
+            CFG.outfile_prefix=[CFG.out_base_temp CFG.NAMES{RUN} '_' num2str(i) '_of_' num2str(CFG.rproc_num_jobs) '.mat'];
+            PAR.CFG=CFG;
+            if CFG.use_rproc
+                fprintf(1, 'Submitting job %i to cluster\n',i);
+                JOB_INFO(JB_NR) = rproc('get_reads_caller', PAR,CFG.rproc_memreq, CFG.rproc_par, CFG.rproc_time); 
+                JB_NR=JB_NR+1;
+            else
+                get_reads_caller(PAR);
+            end
+        end
+        toc   
+    end
+    if CFG.use_rproc
+        [JOB_INFO num_crashed] = rproc_wait(JOB_INFO, 60, 1, -1);
+    end
+end
+
+%%% Generate the output files
+%load the count files
+%load the count files
+READS_PER_GENE=zeros(size(genes,2),size(CFG.BAM_FILES,2));
+GENE_EXPR=zeros(size(genes,2),size(CFG.BAM_FILES,2));
+
+Counts_rDiff_parametric=cell(size(genes,2),size(CFG.BAM_FILES,2));
+Counts_rDiff_nonparametric=cell(size(genes,2),size(CFG.BAM_FILES,2));
+
+
+%Field containing the errors
+ERRORS_NR=[];
+idx=[(1:size(genes,2))',ceil((1:size(genes,2))*CFG.rproc_num_jobs/size(genes,2))']; 
+% Iterate over the result files to load the data from the count files
+for RUN=1:size(CFG.BAM_FILES,2)
+    for j = 1:CFG.rproc_num_jobs
+        IN_FILENAME=[CFG.out_base_temp CFG.NAMES{RUN} '_' num2str(j) '_of_' num2str(CFG.rproc_num_jobs) '.mat'];
+	IDX=idx(idx(:,2)==j,1);
+        try
+            load(IN_FILENAME)
+            for k=1:length(IDX)
+	        %Check wether COUNTS is empty
+		if isempty(COUNTS{k})
+		    continue
+		end
+                %Get the number of reads mapping to a gene
+                if not(isempty(COUNTS{k}{2}))
+                    READS_PER_GENE(IDX(k),RUN)=COUNTS{k}{2};
+                end
+                
+                %get the number of nonalternative reads if
+                %possible. Otherwise use the number of reads
+                %mapping to a gene as gene expression
+                if not(isempty(COUNTS{k}{3}))
+                    GENE_EXPE(IDX(k),RUN)=COUNTS{k}{3};
+                else
+                    GENE_EXPE(IDX(k),RUN)=READS_PER_GENE(IDX(k),RUN);
+                end
+                
+                %get the Counts for rDiff.parametric
+                if not(isempty(COUNTS{k}{6}))
+                    Counts_rDiff_parametric{IDX(k),RUN}=COUNTS{k}{6};
+                end
+                
+                %get the counts for rDiff.nonparametric
+                if not(isempty(COUNTS{k}{4}))
+                    Counts_rDiff_nonparametric{IDX(k),RUN}=COUNTS{k}{4};
+                end
+            end
+        catch
+            warning(['There was a problem loading: ' IN_FILENAME ])
+            % If something went wrong
+            for k=1:length(IDX)
+                READS_PER_GENE(IDX(k),RUN)=0;
+                GENE_EXPR(IDX(k),RUN)=0;
+                Counts_rDiff_parametric{IDX(k),RUN}={};
+                Counts_rDiff_nonparametric{IDX(k),RUN}={};
+            end
+            ERRORS_NR=[ERRORS_NR; [RUN,i]];
+        end
+    end
+end   
+if not(isempty(ERRORS_NR))
+    warning('There have been problems loading some of the raw count files');
+end
+
+%If less than 10 reads use abulute number of reads
+GENE_EXPR(GENE_EXPR<10)=READS_PER_GENE(GENE_EXPR<10);
+
+%Generate gene expression tables
+
+%Open file handler for the gene expression table
+EXPR_TAB_FILENAME=[CFG.out_base 'Gene_expression.tab'];
+fid=fopen(EXPR_TAB_FILENAME,'w');
+
+%print header
+fprintf(fid,'gene');
+for i=1:length(CFG.NAMES)
+    fprintf(fid,'\t%s',CFG.NAMES{i});
+end
+fprintf(fid,'\n');
+
+for j=1:size(genes,2)
+   fprintf(fid,'%s',genes(j).name);
+   for i=1:length(CFG.NAMES)
+       fprintf(fid,'\t%i',GENE_EXPR(j,i));
+   end
+   fprintf(fid,'\n');
+end
+
+fclose(fid)
+
+%Determine interpreter
+if size(ver('Octave'),1)
+    INTERPR = 1;
+else
+    INTERPR = 0;
+end
+
+
+%Save alternative region count file for rDiff.parametric
+OUT_FILENAME=[CFG.out_base 'Alternative_region_counts.mat'];
+if INTERPR
+    save('-mat7-binary',OUT_FILENAME,'Counts_rDiff_parametric')
+else
+    save(OUT_FILENAME,'Counts_rDiff_parametric','-v7.3')
+end
+
+%Save alternative region count file for rDiff.nonparametric
+OUT_FILENAME=[CFG.out_base 'Nonparametric_region_counts.mat'];
+if INTERPR
+    save('-mat7-binary',OUT_FILENAME,'Counts_rDiff_nonparametric')
+else
+    save(OUT_FILENAME,'Counts_rDiff_nonparametric','-v7.3')
+end
+
+return