#!/usr/local/bin/perl
use strict;
use warnings;
use Data::Dump qw(pp);
use feature qw(switch say);

my $path = "testSample.txt";
open(FH, $path) or die("error, $!\n");
my (%hetero, %homo, %unclassified);
until(eof(FH)){
       my ($file, $patientName, $panel, $snp, $allele1, $allele2, $size1, $size2)= split "\t", <FH>;
        $snp ||='';$allele1 ||= ''; $allele2||=''; #if not initialized set to ''
        chomp($snp);
        $snp = 'missed' if $snp eq '';
        given($allele1, $allele2){
                when($allele1 ne '' && $allele2 ne ''){constructHetero($snp, $patientName, $allele1, $allele2)}
                when($allele1 ne '' && $allele2 eq ''){constructHomo('type1', $snp,$patientName, 'allele1', $allele1)}
                when($allele1 eq '' && $allele2 ne ''){constructHomo('type2', $snp,$patientName, 'allele2', $allele2)}
                when($allele1 eq '' && $allele2 eq ''){constructUnclassified($snp, $patientName)}
                }
    }

sub constructHetero{
        my ($snp, $patientName, $allele1, $allele2) = @_;
        $hetero{$snp}{$patientName}{'allele1'}=$allele1;
        $hetero{$snp}{$patientName}{'allele2'}=$allele2;
        $hetero{$snp}{$patientName}{'records'}++;
        $hetero{$snp}{'total_records'}++;
        };

sub constructHomo{
        my ($type, $snp, $patientName, $alleleNumber,$allele)=@_;
        $homo{$type}{$snp}{$patientName}{$alleleNumber}=$allele;
        $homo{$type}{$snp}{$patientName}{'records'}++;
        $homo{$type}{$snp}{'total'}++;
        $homo{$type}{'total_records'}++;
        }
        
sub constructUnclassified{
        my($snp, $patientName)=@_;
        $unclassified{$snp}{$patientName}{'records'}++;
        $unclassified{$snp}{'total'}++;
        $unclassified{'total_records'}++;
        }

#print pp(\%hetero);
#print pp(\%homo);
#print pp(\%unclassified);

##</code><code>##

testSample.txt
Sample File	Sample Name	Panel	SNP	Allele 1	Allele 2	Size 1	Size 2
011.fsa	MS-039	Panel_3130
012.fsa	MS-039	Panel_3130					31.76
014.fsa	MS-291	Panel_3130	rs7577363			90.79	92.46
013.fsa	MS-291	Panel_3130	rs7577363
006.fsa	MS-290	Panel_3130	rs10735781		G	78.69	80.31
005.fsa	MS-290	Panel_3130	rs10735781		G	78.85	80.32
011.fsa	MS-039	Panel_3130	rs10735781	C		78.63	80.1
001.fsa	MS-148	Panel_3130	rs10735781	C	G	78.57	80.2

##</code><code>##