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string sourcePath = "source.pdf";
string targetPath = "target.pdf";
string resultPath = "source.pdf";
//do not compare header/footer
CompareOptions compareOptions = new CompareOptions();
compareOptions.HeaderFootersComparison = false;
Comparer comparer = new Comparer(sourcePath);
comparer.Compare(File.Create(resultPath), new SaveOptions(), compareOptions);
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