#!perl
use strict;
use 5.010;
my $STARFile;																				# File handle to reference file
my @Stars;
$Stars[0] = "CYP2C19_10";																	# Mock array of values to cross reference
$Stars[1] = "CYP2C19_12";																	#


if(@Stars==0){return;}																		# If no Star Alleles were specified then no need to do this so return to the main body

if(! open $STARFile,"<","test.csv"){die "Reference file could not be found or could not be opened.";}	# Open the Star reference file to prepare to convert information and store the file handle to $STARFile.
print "Converting specified Star Designations to SNPs...";
# The conversion table is opened so convert the Star name to rs numbers and then store the rs numbers to the @SNPs array and the corresponding Star name to the @Stars array at the same index.
my @SNPs;
my @StarsCon;
my $RefIndex;																				# Holds the line in the reference table file
my $StarIndex;																				# Holds the index of the @Stars Array that is being checked
my $tmpSNPIndex;																			# Holds the index in the @SNPs array that we are comparing
my $tmpStar;																				# Holds the Star Allele name
my $tmpRS;																					# Holds the SNP's rs number
my @tmpConv;																				# Holds the split Star and rs numbers
say "\n--------- Converting Star Allele references to rs numbers ---------";
while (<$STARFile>){																		# Input a line from the database and  as long as we haven't reached the end of the file
	chomp;																					# Remove the trailing newline
	say "Current input line is @_";
	@tmpConv = split ",",$_;																# Split the CSV line from the reference table such that @tmpConv[0] = Star name and @tmpConv[1] = rs number
	$tmpStar = $tmpConv [1];
	$tmpRS = $tmpConv[0];
	say "Index 0 is $tmpConv[0]";															# Displays correctly
	say "Index 0 is $tmpConv[0] is stored as $tmpRS";										# Displays correctly
	say "Index 1 is $tmpConv[1]";															# Displays correctly
	say "Index 1 is $tmpConv[1] is stored as $tmpStar";										# Displays INcorrectly

	for($StarIndex=0;$StarIndex<@Stars;$StarIndex++){
		say "Comparing $tmpStar and $Stars[$StarIndex]";
		if($tmpStar eq $Stars[$StarIndex]){													# If the current line of the database file contains the Star Allele rs number then
			$tmpSNPIndex = @SNPs;															# Get the number of entries in the @SNPs array.
			say "1. $tmpRS was converted from $tmpStar";
			say "2. $tmpStar was converted to $tmpRS";
			
			say "3. $tmpStar was converted to $tmpRS";
			say "4. $tmpRS was converted from $tmpStar";
			
			push @StarsCon, $tmpStar;														# Add the Star allele name to the @StarsCon array
			push @SNPs, $tmpRS;																# Add the new rs number to the @SNPs array
			if(@Stars>0){																	# If we have more than one SNP then
				splice @Stars,$StarIndex,1;													# and @Stars array
			}else{																			# Otherwise Pop off the last one
				pop @Stars;																	#
			}
			last;																			# Exit the for loop
		}
	}
	if(! @Stars>0){last;}																	# If that was the last entry then stop searching
}
say "-------------- Done converting Star Allele references -------------";
if(@Stars>0){																				# If any SNPs have not been found then 
	say "\n"."Conversions not completed: @Stars.";											# Inform the user which ones were not found
}else{																						# Otherwise
	say "\n"."All conversions successful.";													# Inform the user that all were found
}
close $STARFile;																			# Close the reference file
print "Done!\n";