in reply to 'Invisible' newlines/line wrapping
Show us some code that we can run and the demonstrates the issue. There is nothing in the code you show that would generate the effect you describe unless the contents of $index is not what you expect it to be. Is it possible that you read the contents of $index from a file and it still has a trailing new line for example? A common error is to do something like:
while (<$inFile>) { my ($this, $that, $theOther, $index) = split; }
and miss chomping before the split.
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