Sat Jan 30 17:39:46 PST 2010
Task: Unify the way of handling different short reads
	1. Build virtual segments, calculate the probability of a randomly sampled
	read falling into a virtual segments. Call the maximum likelihood method
	by HuiJiang.

	2. Modify the class Instance and the format of the instance file.
	Therefore the InstanceReader and InstanceWriter should be modified
	accordingly. The format of the instance file will be

### Old example                                                                                                 ### New example
	Instance	1	8	3	3	                                                                                
	read len  :	25                                                                                              
	read cnt  :	40000000                                                                                        
	cross str :	3                                                                                               
 	noise lev :	0                                                                                               
 	genes     :	3                                                                                               
 	uc007aet.1	chr1	-	3195984	3205713	3195984,3203519	3197398,3205713                                     
 	uc007aeu.1	chr1	-	3204562	3661579	3204562,3411782,3660632	3207049,3411982,3661579                     
 	uc007aev.1	chr1	-	3638391	3648985	3638391,3648927	3640590,3648985                                     
 	exp segs  :                                                                                                 
 	chr1	+	3195984	3197398	15	15	15	0	1                                                               
 	chr1	+	3203519	3204562	9	9	9	0	0                                                               
 	chr1	+	3204562	3205713	127	121	121	0	1                                                               
 	chr1	+	3205713	3207049	112	117	111	1	1                                                               
 	chr1	+	3411782	3411982	20	19	18	0	1                                                               
 	chr1	+	3638391	3640590	0	0	0	0	1                                                               
 	chr1	+	3648927	3648985	0	0	0	0	1                                                               
 	chr1	+	3660632	3661579	94	96	94	0	1                                                               
 	fit value :	     0	     0	     0	     0	     0	     0	     0	     0                                  
	sample cnt:	    15	     9	   121	   111	    18	     0	     0	    94                                  
	set size  :	  1414	  1043	  1151	  1336	   200	  2199	    58	   947                              	
	iso     0	     1	     1	     1	     0	     0	     0	     0	     0	 0.011                      	
	iso     1	     0	     0	     1	     1	     1	     0	     0	     1	0.0935                      	
	iso     2	     0	     0	     0	     0	     0	     1	     1	     0	2.67e-05                    	
					 0	     0	     0	     0	     0	     0	     0	     0                              	
					 0	     0	     0	     0	     0	     0	     0	     0                              	
					 0	     0	     0	     6	     0	     0	     0	     0                              	
					 0	     0	     0	     0	     1	     0	     0	     0                              	
					 0	     0	     0	     0	     0	     0	     0	     2                              	
					 0	     0	     0	     0	     0	     0	     0	     0                              	
					 0	     0	     0	     0	     0	     0	     0	     0                              	
					 0	     0	     0	     0	     0	     0	     0	     0                              	
	PE info:	20	300	30	5057233	6                                                                           
	0	0	0	1	1	0	0	1	1                                                                           
	0	0	1	1	0	0	0	0	8                                                                       	
	0	0	0	1	1	0	0	0	7                                                                       	
	1	1	0	0	0	0	0	0	3                                                                       	
	0	0	0	0	1	0	0	1	5                                                                       	
	0	0	0	1	0	0	0	1	2                                                                       	
	 0	     0	     0	     0	     0	     0	     0	     0                                                  
	 0	     0	     0	     0	     0	     0	     0	     0	    											
	 0	     0	     0	     2	     0	     0	     0	     0                                                  
	 0	     0	     0	     0	     0	     0	     0	     0                                                  
	 0	     0	     0	     0	     0	     0	     0	     1                                                  
	 0	     0	     0	     0	     0	     0	     0	     0                                                  
	 0	     0	     0	     0	     0	     0	     0	     0                                                  
	 0	     0	     0	     0	     0	     0	     0	     0                                                  
	SE exons:	3                                                                                               
	0	2                                                                                                       
	2	7                                                                                                       
	5	6                                                                                                       
                                                                                                            	
                                                                                                            	
                                                                                                                
                                                                                                                
																											    
                                                                                                                
                                                                                                                
                                                                                                                
                                                                                                                 

	Modification Detail:
	* Define a class for each read type
	* Modify the pattern description
	* Modify class Instance
	* Modify class InstanceReader
	* Modify class InstanceWriter
	* Modify loading-read functions in DataProcess
	* Modify the class RandomExpReadAssignerIM
	* Modify class Exon
	* Modify InstanceWriter::WriteHui
	* Remove the job of gen_hui, Add the option of using HuiJiang's code to
	calculate expression levels.
	* Modify the interfact of describing read info file
	* Modify DataProcess::HighIsoforms


Instance	1




genes 3
uc007aet.1	chr1	-	3195984	3205713	3195984,3203519	3197398,3205713
uc007aeu.1	chr1	-	3204562	3661579	3204562,3411782,3660632	3207049,3411982,3661579
uc007aev.1	chr1	-	3638391	3648985	3638391,3648927	3640590,3648985
segs 8
chr1	+	3195984	3197398	0	1
chr1	+	3203519	3204562	0	0
chr1	+	3204562	3205713	0	1
chr1	+	3205713	3207049	1	1
chr1	+	3411782	3411982	0	1
chr1	+	3638391	3640590	0	1
chr1	+	3648927	3648985	0	1
chr1	+	3660632	3661579	0	1
isoforms 3
K 1	     1	     1	     0	     0	     0	     0	     0	 0.011
U 0	     0	     1	     1	     1	     0	     0	     1	0.0935
U 0	     0	     0	     0	     0	     1	     1	     0	2.67e-05
Reads          
0 11          # <Single-end reads with constant lengthes> <Read length> <Read cnt> <Pattern cnt>
1 1	?
1 2	?
1 3	?
1 4	?
1 5	?
1 6	?
1 7	?
1 8	?
2 1 3	?
2 2 3	?
2 5 7	?
Reads 1                   
0 11          # <Single-end reads with varying lengthes> <Pattern cnt>
1 1	?
1 2	?
1 3	?
1 4	?
1 5	?
1 6	?
1 7	?
1 8	?
2 1 3	?
2 2 3	?
3 5 7 8	?
Reads 2        
0 11          # <Paired-end reads with varying lengthes> <Pattern cnt>
3 4 5 7 1     # <#Segments involved> <Segments> <#Reads on this pattern>
2 2 3 8
2 3 4 7
2 1 2 3
2 4 7 5
2 3 7 2
SESegs 3
0	2        
2	7        
5	6        


