Start by trimming your input data in half until you find a minimal set of input that causes the issue.

If you don't see a bad entry in the input remaining, then sprinkle some print statements through your code, and see where and when that undef is appearing.

PS: If you rewrite 

for($i=0; $i<=$#split_aligns_non_barrel; $i++)
{
$separate_hit_non_barrel=$split_aligns_non_barrel[$i];
...

[download]
as 
for my $separate_hit_non_barrel (@split_aligns_non_barrel)
{
...

[download]
Then that would simplify your code a fair bit and make it easier to read. Fewer pseudo-global variables and unnecessary worrying about indexes is good too.

In reply to Re: Can you tell me why I get this error and if I can optimize my code somehow? by SuicideJunkie
in thread Can you tell me why I get this error and if I can optimize my code somehow? by Anonymous Monk

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