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How can I use pgn-extract to remove a game from a pgn file when there is an illegal move?

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pgn-extract will do exactly that if you give it an input file and say where you want the correct games to go. For instance:

pgn-extract --output clean.pgn games.pgn

will put only the valid games from games.pgn into clean.pgn, reporting any errors on standard output. If you want to have a record of the errors then you can use the -l flag to specify a log file; e.g.:

pgn-extract --output clean.pgn -lissues.txt games.pgn

There are lots of additional options/flags described in the documentation.

Disclosure: I am the author of pgn-extract.

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