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@haplotypes = (); ## THIS IS AN ARRAY DECLARATION
.....
push @{ $haplotypes{ $currentPop} }, [ @temp ];
## THIS ...........^............^...................is a hash
## with a numeric key, that increments from zero, by 1!
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@temp = split;
push @{$haplotypes{$currentPop}}, [@temp];
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push @{ $haplotypes[ $currentPop ] }, [ split ];
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@{$TempList{$currentPop};} = ();
while (@{$haplotypes{$currentPop};}) {
push @{$TempList{$currentPop};}, splice(@{$haplotypes{$current
+Pop};}, rand @{$haplotypes{$currentPop};}, 1);
}
@{$haplotypes{$currentPop};} = @{$TempList{$currentPop};};
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use List::Util qw[ shuffle ]; ## near the top of your program.
...
@{ $haplotypes{$currentPop } } = shuffle @{ $haplotypes{$currentPo
+p } };
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push @total, $currentPop;
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for($i = 0; $i < $sampleSize{$_}/2; $i++) {
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Use of uninitialized value in division (/)...