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java -cp readseq.jar run NC_012967.1.gbk -f GFF -o test.gff
java -cp readseq.jar run NC_012967.1.gbk -f GFF -o NC_012967.1.gbk.gff
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It's a bit hard to figure out because it takes the unnamed arguments before the optional flag arguments and there is no example command and you have to switch -jar to -cp. Search online for usage examples when you can't figure something out from the help.
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