--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tools/sanitize_genes.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,95 @@
+function [genes]=sanitize_genes(genes,CFG)
+%This function removes trnascript and genes which have a invalid
+%structure and recomputes the splicegraph
+
+
+%Mark genes with eronous exon definitions
+RM_GENES_IDX=[]; %genes to keep
+for i=1:size(genes,2)
+  %remove transcripts which have a length smaller than
+  %readlength
+  RM_TR_IDX=[];
+  START_MIN=inf;
+  STOP_MAX=0;
+  for j=1:size(genes(i).transcripts,2)
+    if sum(genes(i).exons{j}(:,2)-genes(i).exons{j}(:,1))< CFG.sequenced_length
+      RM_TR_IDX=[RM_TR_IDX,j];
+    else
+      START_MIN=min(START_MIN,genes(i).exons{j}(1,1));
+      STOP_MAX=max(STOP_MAX,genes(i).exons{j}(end,2));
+    end 
+  end
+  if ~isempty(RM_TR_IDX)
+     genes(i).exons(RM_TR_IDX)=[];
+    genes(i).transcripts(RM_TR_IDX)=[];
+    genes(i).start=START_MIN;
+    genes(i).stop=STOP_MAX;
+  end
+  if genes(i).start>START_MIN
+      genes(i).start=START_MIN;
+  end
+  if genes(i).stop<STOP_MAX
+      genes(i).stop=STOP_MAX;
+  end
+  
+  
+  %Check if exons are eronous
+  CHECK=1;
+  
+  if size(genes(i).transcripts,2)==0
+    CHECK=0;
+  end
+  
+  for j=1:size(genes(i).transcripts,2)
+    for k=1:(size(genes(i).exons{j},1)-1)
+      if (genes(i).exons{j}(k,2)> genes(i).exons{j}(k+1,1))
+	CHECK=0;
+	break;
+      end
+    end
+    
+    if isempty(genes(i).exons{j})
+	CHECK=0;
+	break;
+    end
+    if CHECK==0
+      break
+    end
+  end
+  
+  if genes(i).stop-genes(i).start<=CFG.sequenced_length
+    CHECK=0;
+  end
+  if CHECK==0
+    RM_GENES_IDX=[RM_GENES_IDX;i];
+    genes(i).do_not_quant=1;
+  else
+      genes(i).do_not_quant=0;
+  end
+end
+%genes(RM_GENES_IDX)=[];
+
+% Create splicegraph 
+for i=1:size(genes,2)
+  gene=genes(i);
+  ALL_EXO=[];
+  
+  for j=1:size(gene.exons,2)
+    ALL_EXO=[ALL_EXO;gene.exons{j}];          
+  end
+  ALL_EXO=unique(ALL_EXO,'rows');
+  GRAPH=zeros(size(ALL_EXO,1),size(ALL_EXO,1));
+  for j=1:size(gene.exons,2)
+    for k=1:(size(gene.exons{j},1)-1)
+      [A,B]=intersect(ALL_EXO,gene.exons{j}(k,:),'rows');
+      [A,C]=intersect(ALL_EXO,gene.exons{j}(k+1,:),'rows');
+      GRAPH(B,C)=1;
+    end
+  end
+  GRAPH=GRAPH+GRAPH';
+  genes(i).splicegraph{1}=ALL_EXO';
+  genes(i).splicegraph{2}=GRAPH;
+end
+
+
+  
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