uninitialised values in StartWithBestScore script

[duartemolha]

if you run your test scripts on you test data included on the repo you come across un-initialized values for the @calcSampleRatio
line 1173

I believe the issue is on the for loop starting on line 1168

        foreach my $idxKeep (@idxToKeep){ #Iterate over indices to keep
            push(@calcSampleRatio, $sampleRatio[$idxKeep]); #Push sample CVs to calculate mean and sd on into new array
        }

May I suggest an edit :

        foreach my $idxKeep (@idxToKeep){ #Iterate over indices to keep
            if (defined $sampleRatio[$idxKeep]){
                push(@calcSampleRatio, $sampleRatio[$idxKeep]); #Push sample CVs to calculate mean and sd on into new array
            }else{
                print STDERR "Sample index undef\n";
            }
        }