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You probably do NOT want to use Calibre to read PDF files - just to store and index them. The reason is that if you ask Calibre to use its own viewer for PDF files, it first internally converts them to ePub, and then opens the result in the Calire viewer (which is really just an ePub viewer). This has the disadvantages that the conversion can take some time, and often PDF->Epub conversions do not work well.
What you would be better doing is to tell Calibre (as mentioned earlier) to use your system level viewer for PDF files. You then get the same viewer whether you open the PDF file from within Calibre or externally to Calibre.
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