#!/usr/bin/perl 

use strict;
use File::Find;
use Parallel::ForkManager;


my @toParse; # array of chip files

foreach(@toParse){ 

    my $encryptKey = $_;    #Encrypted for patients
    my @name = split /\//, $fileManifest{$encryptKey}; #hash contains the directories
    my $id = pop(@name); # @name is an array of the directory, last element is the sample ID
    my $perlOut = join "\/",@name; # directory for perl commands 
    my @safeID = split / /, $id; 
    my $safeDirect = $perlOut."/".$safeID[0]; # hipaa compliant 
		
    next if($safeID[0 ] =~ /cgo/ig);


#-----------------------------------------------------------------
#	Prepare the commands for conversion									 	
#-----------------------------------------------------------------
		
    my $cychpCommand = $fileManifest{$encryptKey}; #directory of the cychp file
    $cychpCommand =~ s/\//\\/g; # Format the directory for windows and for the affy program
    $cychpCommand = "\"".$cychpCommand."\"";
			
    my $cychpTxtOut = join "\\", @name;	#CYCHP TXT OUTPUT DIRECTORY 
    $cychpTxtOut ="\"".$cychpTxtOut."\"";																	 	
    my $affyCommand = "apt-chp-to-txt -o ".$cychpTxtOut." ".$cychpCommand;
    
    unless(exists($cychpLog{$encryptKey})) {
					
        my $rmCom = $perlOut."/apt-chp-to-txt.log";
			
	push @toConvert1, $affyCommand; # To send commands for conversion
	push @toConvert2, $rmCom; # To remove the log files
					
	$cychpLog{$encryptKey}++;
 	$timestamp = localtime(time);
 	open LOG, ">>".$logFileName;
 	print LOG "$encryptKey\t$safeID[0]\t$safeDirect\t-\t-\t$timestamp\n";
 	close(LOG);
						
	}	
}

#-----------------------------------------------------------------
#	Begin forking											
#-----------------------------------------------------------------
	
my $maxProcs = scalar(@toConvert1);
my $pm = new Parallel::ForkManager($maxProcs);

foreach(@toConvert1){
		
    my $pid = $pm-> start and next;		# FORK Begin
    system($_); #	CONVERSION COMMAND
    $pm->finish;	# End of FORK

}
	
$pm->wait_all_children; # Blocks until all children are finished 

foreach(@toConvert2){
    unlink $_; #Delete log files made by the conversion program
}

foreach(@toParse){
    my $txtFile = $_.".txt";
    open IN, $txtFile or die "Cannot open [$txtFile]\n";
   
    while(<IN>){
       parsing happens here
    }

}