General patents aren't allowed.

If there wasn't a specific limitation against software patents, you could patent the process of "first we look at the first 3 bytes for a BOM, then we take statistics of the most frequently used bytes and match them against this table..." which is the software equivalent of "the device contains a large box full of water, underneath which is a flame and on the upper side is a pipe leading to a valve box which contains..."

Either one would still have to meet the requirements like being sufficiently non-obvious. The first steam engine was patented, even though you couldn't patent one any more.