--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/get_reads_caller.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,150 @@
+function [COUNTS]=get_reads_caller(PAR)
+
+CFG = PAR.CFG;
+genes = PAR.genes;
+clear PAR;
+
+% add paths
+addpath(CFG.paths);
+
+data_dir=CFG.data_dir;
+OUT_STR=[];
+
+COUNTS=cell(size(genes,2),1);
+
+
+% NON_PARAM_SAMPLE contains the read start density 
+if CFG.perform_nonparametric
+    NON_PARAM_SAMPLE=sparse([],[],[],10000,1,5000);
+end
+
+
+for i=1:size(genes,2)
+  
+    
+      
+  %TEMP_COUNT contins the counts for the current gene
+  TEMP_COUNT=cell(1,7);
+  gene = genes(i);
+  
+  %set default return values
+  TEMP_COUNT{1}=gene.name;
+  TEMP_COUNT{2}=[];
+  TEMP_COUNT{3}=[];
+  TEMP_COUNT{4}=[];
+  TEMP_COUNT{5}=[];
+  TEMP_COUNT{6}=[];
+  
+  %check that the gene has exons defined
+  if isempty(gene.exons)
+    STAT{i}=TEMP_COUNT;
+    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
+    STAT{i}=TEMP_COUNT;
+    continue;
+  end
+  
+  %Get the reads from gene
+  [reads] = get_reads_for_gene(CFG,gene);
+
+ 
+  %Get total number of reads
+  NR_OF_READS=size(reads,1);
+  TEMP_COUNT{2}=NR_OF_READS;
+  
+ 
+  NR_OF_TRANS=size(gene.transcripts,2);
+  %check that the gene has more than one isoform
+  if NR_OF_TRANS<=1
+      STAT{i}=TEMP_COUNT;
+      continue;
+  end
+ 
+  
+  EXON_IDX=sum(gene.exonsequence,1)<NR_OF_TRANS;
+
+  %Transform the reads in to counts per region
+  [NEW_READS,UNEXPLAINED_READS,UNEXPLAINED_INDEX]= convert_reads_to_region_indicators(reads,gene);
+
+  if length(unique(sum(NEW_READS,2)))>1
+      warning(['Assignment of reads to regions is not unique for gene:' gene.name  '\n']); 
+  end
+  
+  
+  %Calulate gene expression
+  %Get the non_unique_regions
+  NON_ALT_EIRS=sum(gene.eirs_in_seq,1)==NR_OF_TRANS;
+  TEMP_COUNT{3}=sum(sum(NEW_READS(:,NON_ALT_EIRS),2)>0); 
+  
+  
+  %Get Counts for nonparametric variance function
+  if CFG.perform_nonparametric
+      %Get the read starts
+      [TEMP,START]=max(reads,[],2); 
+      read_starts=sparse((1:NR_OF_READS)',START,ones(NR_OF_READS,1),NR_OF_READS,size(reads,2),NR_OF_READS);
+      
+      %Get the index of the alternative reads
+      ALT_READ_IX=zeros(size(reads,1),1);
+      ALT_EIRS=and(sum(gene.eirs_in_seq,1)<NR_OF_TRANS,sum(gene.eirs_in_seq,1)>0);
+      ALT_READ_IX(UNEXPLAINED_INDEX==0)=sum(NEW_READS(:,ALT_EIRS),2)>0;
+      
+      %Get the coverage of the read starts
+      %COVERAGE=sum(read_starts(find(ALT_READ_IX>0),:),1);
+      if CFG.only_gene_start
+          COVERAGE=sum(reads,1);
+      else
+          COVERAGE=sum(reads(find(ALT_READ_IX>0),:),1);
+      end
+      if max(COVERAGE)>0
+          TEMP_COUNT{4}=COVERAGE;
+      else
+          TEMP_COUNT{4}=[];
+      end 
+  end
+  
+  
+  %Get counts for parametric settting
+  if or(CFG.perform_parametric,CFG.perform_poisson)
+      %Get the alternative reads 
+      ALT_EIRS=and(sum(gene.eirs_in_seq,1)<NR_OF_TRANS,sum(gene.eirs_in_seq,1)>0);
+      
+      %Return the Counts in the alternative EIRS
+      
+      COUNTS_PER_EIR=sum(NEW_READS(:,ALT_EIRS),1);
+      EXS_SEQ=gene.eirs_in_seq(:,ALT_EIRS);
+      [NEWCOLS,IDX2,POS]=unique(EXS_SEQ','rows');
+      NEWCOLS=NEWCOLS';
+      EIR_COUNTS=zeros(1,length(IDX2));
+      for j=1:max(POS)
+          EIR_COUNTS(j)=sum(COUNTS_PER_EIR(POS==j));
+      end
+      TEMP_COUNT{6}=EIR_COUNTS;
+  end
+  
+  clear NEW_READS
+  clear reads;
+  COUNTS{i}=TEMP_COUNT;
+  
+  OLD_OUT_STR=OUT_STR;
+  OUT_STR=['Finished ' num2str(i) ' out of ' num2str(size(genes,2)) ' genes'];
+  %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
+  
+  
+end
+fprintf('\n')
+%Save the counts
+OUT_FILENAME=[CFG.outfile_prefix];
+save(OUT_FILENAME,'COUNTS')
+%Save the nonparametric histogram
+