* Genotype Tools Kit: Merge
* Daniel E. Cook 2011
program define ccmatch
    version 11.0
    syntax varlist [if] [in] [, cc(name) id(name)]
	tempvar match randorder ucc

quietly generate `match' = ""
foreach var in `varlist' {
capture confirm numeric variable `var'
if !_rc {
	quietly replace `match' = `match' +  string(`var') + "_" 
}
else {
	quietly replace `match' = `match' + `var' + "_" 
}
}


//  Generate a random variable for sorting purposes.
generate `randorder' = runiform()

local max = _N

// Sorts data randomly.
sort `match' `cc' `randorder'

// Generate variables if we don't have them already.
capture confirm variable match_id 
if !_rc {
	drop match_id
}
	// Generate Match ID var. based on type of id (numeric or string)
capture confirm string variable `id'
	if !_rc {
		quietly generate match_id = ""
		noisily di "string created"
		} 
		else {
		quietly generate match_id = .
		noisily di "numeric created"
	}

	
// Generate variables if we don't have them already.
capture confirm variable matched_pair 
if !_rc {
	drop matched_pair
}
// Generate matched pair
generate matched_pair = .

// Generate a numerical variable for case/control if need be.
capture confirm numeric variable `cc'
if _rc {
	quietly encode `cc', generate(`ucc')
	quietly replace `ucc' = `ucc' - 1
}
else {
	quietly generate `ucc' = `cc'
}

foreach obs of numlist 1/`max' {
	if `ucc'[`obs'] == 0 {
		quietly count if `match' == `match'[`obs']
		local traverse_amount =`r(N)'
		foreach moveup of numlist 1/`traverse_amount'	{
		local match_obs = `obs' + `moveup' - 1

			if (`match'[`obs'] == `match'[`match_obs']) & `ucc'[`match_obs'] == 1 & matched_pair[`obs'] == . & matched_pair[`match_obs'] == .{
			quietly {
				local pair = `pair' + 1 // The Pair Counter
				local pair_obs = `obs'+`moveup' - 1
				replace match_id in `obs' = `id'[`match_obs']
				replace match_id in `match_obs' = `id'[`obs']
				replace matched_pair in `obs' = `pair'
				replace matched_pair in `pair_obs' = `pair'
				}
			
			
			
			
			}
		}
	}
}

sort matched_pair
order match*
di 
di "Total Matches: `pair'"



end