Sometimes it is hard to beat several decades of development... The classical Unix command line tools written in 'C' should be quite fast in exexuction and development: 
sort --merge --unique fileA fileB > output

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If disk space is your major concern, I'd instead compress the input and output files. Text files typically compress to 10% of their initial size. Your command line could then be 
zcat fileA.gz fileB.gz | sort --merge --uniq --compress-prog= gzip | g
+zip > output.gz

[download]
Both commands need some disk space in /tmp or in --temporary-directory. RAM usage can be fine tuned with --bufer-size. You'll find out about the --key option by yourself.

In reply to Re: Delete lines as i read them by NiJo
in thread Delete lines as i read them by pie-ence

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