Dotan> The regex seems to be catching more than I would expect it to:
    ...

Worked for me.  The directory I ran the script in had your sample and one
other VCF file.  It made the apparently correct changes to yours.  The other
was unchanged.

    Dotan> Why is that? I tried to fix it, but I do not even see what is
    Dotan> wrong to fix! It looks god to me.

Just out of curiosity, are the line endings CRLF perchance?  If so, try
changing the replace call like this:

    cooked = uncooked.replace('\r\n ', '')

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