Reshuffle ver 0.000

Parameters:

The first parameter tells the name of CLACK-GWAS output file (without iout 
and out extensions), for example, the first parameter must be 

	B_myeigen
	 
if CLAK-GWAS output files are B_myeigen.iout and B_myeigen.out

A number of options allow to extract different types of information from 
CLAK-GWAS outputs. 

Data dimensions are obtained by adding option  

	--datadims
	
which gives back t (number of traits), m (number of markers), p (number of 
covariates + 2); the information is stored in a file named "datadims.txt"

SNP names
	default: (--snpnames) : all
	by index (--snpnames=27) : name of snp#27
	by index range, combination (--snpnames=27,2-12,4-20) : name of snp #2-20,27
output: "snpnames.txt"
	
Trait names 
	default (--traitnames): all
	by index (--traitnames=27) : name of trait #27
	by index range, combination (--traitnames=27,2-12,15)
output: "traitnames.txt"

Heritabilities, sigma, res_sigma, estimates
	Default: (--heritabilities) : all traits
	Reange,indexes (--heritabilities=1-10,4,5-12) : for traits #1-12
	trait's names (--heritabilities=hgta,hdla) : for traits hgta,hdla
	regexp in trait's names (--heritabilities=regexp=t) : for traits, in the start of which is "t" : tga,tca (in data_4test)
	all combinations (--heritabilities=1-10,4,5-12,hgta,lipid_tca,regexp=lipid_)
output: "estimates.txt"	
Results - association
	by SNP
		Dafault (--snp) : for all snp for all traits
		indexes, ranges (--snp=12,100-1000,500-10000,22000) :  for all traits
		names (--snp=rs3121561,rs6687776) : for snps rs3121561,rs6687776
		names+around (--snp=rs3121561,rs6687776,before=10,after=15)
			for  (-10,9,...,-1,rs3121561,1,2,...,15,16) + (-10,9,...,-1,rs6687776,1,2,...,15,16)
		indexes+names+focus (--snp=1-20,50,rs3121561,rs6687776,before=10,after=15)
			for snps : #1-20,50 + (-10,9,...,-1,rs324001,1,2,...,15,16) + (-10,9,...,-1,rs123123,1,2,...,15,16)
			NB!: focus only for snp's names, not for indexes
	output: "data.txt"
	by trait
		Dafault (--trait) : for all snp for all traits
		indexes,range (--trait=1-10,12) : for snp #12 for all traits
		by names (--traits=tca,hdla) : for traits tca,hdla
		regexp in trait's names (traits=regexp=lipids_) : for all traits, which name in the beginig has "lipids_"
		all combinations
	output: "data.txt"
	Chi2 more than some threshold
		(--chi=20) for snps,which chi>20 for all traits
	output: "chi_data.txt"
	All combinations of traits,snps, Chi2
		(--traits=1-2--snps=1-1000--chi=15) for traits #1-2 for snps#1-1000, which chi>15
		output: "chi_data.txt"
		
Just write data with chi
	(--chi) : write data(with chi column) for all snps for all traits
	all combinations are supported
	output: "chi_data.txt"
Dataslim
	Creating a sub-matrix by Chi2>X (--chi=X--dataslim)
	output: "slim_data.txt"
	
Test
	(--test) run all tests
	output: test.txt
	
Info 
	(--info) write some information about programm's run

Examples:
Reshuffle.exe B_1112_NA_clear_RNA_nocovar --traitnames=1-4,1--snpnames=1-10,20-30,46--traits=1--snps=1-100

outputs from B_1112_NA_clear_RNA_nocovar.iout and B_1112_NA_clear_RNA_nocovar.out:

	traitnames.txt : with trait's names hgta,tga,tca,ldla
	snpnames.txt Names of snps #1-10,20-30,46
	trait_hgta.txt : result of association for trait "hgta" for snps #1-100