Readme for BOOST 2.0

BOOST 2.0 is a multi-threaded implementation of the advanced BOOST method (with covariates adjustment). BOOST 2.0 has been tested on a machine with Windows 10 system. If you encounter any problem about using BOOST 2.0, you are welcome to contact the author at mwangaq@connect.ust.hk.


===== Recommended platform, software version and hardware for BOOST 2.0=====================
CPU: Intel(R) Core(TM) i5-4570 CPU 3.20 GHz 
Main Memory: 4 GB or above                        
Operation System: Windows 10 x64


===== Compiling ======================================================================
In Windows, we use Visual studio 2015 to compile and build the executable file. Put the 5 files: main.cpp, utility.cpp, postCorrec.cpp, interactionCal.cpp and utility.h in the Visual Studio project and we will be able to build it.


===== Program Usage ======================================================================
Usage is 
	BOOST2  -i inputfilelist.txt -n numofCov -nt numofThreads -tt testThreshold -o outputprefix
		-i  Input List File
		-n  Number of Covariates Considered
			Default : 1
		-nt Number of Threads in Use
			Default : 1
		-tt Test Threshold
			Default : 30.0 
		-o  Output File Prefix
			Default : ""

Examples : 
	The sample data "example_simu.txt" is for one covariate case. Users can use following command.
	
	BOOST2 -i filenamelist.txt -n 1 -nt 4 -tt 40 -o output_
	
	The program will output interaction record file 
		'output_InteractionRecord.txt' 



====Input File Format========================================================================
Input file is a n*(p+ncov+1) matrix, where n is the number of samples, p is the number of SNPs, ncov is the number of covariates taken into consideration, the extra "1" is the phenotype. Phenotype must be the first digit in each row.
	Example:
		Phenotype Cov1 Cov2 SNP1 SNP2 SNP3 SNP4 SNP5 ...
   sample1	0           1	 1    2    0    1    2    1
   sample2	1	    0    1    1    1    2    0    1 	



====Output File Format========================================================================
	Example:
		Pair_index  SNP1  SNP2 	 Statistic_test_value
		Pair No.0:    0    1           31.1396
