Cuneiform outputs both boundingboxes:

<p><span class='ocr_line' id='line_1' title="bbox 36 93 580 123">This is
a lot of 12 point text to test the <span class='ocr_cinfo'
title="x_bboxes 36 93 55 117 57 93 71 117 ... [and so on and so on]

The line is in the first span and the letters in the second.

-- 
Font size not correct in merged sandvich PDF
https://bugs.launchpad.net/bugs/623438
You received this bug notification because you are a member of Cuneiform
Linux, which is the registrant for Cuneiform for Linux.

Status in Linux port of Cuneiform: Invalid

Bug description:
After processing with Cuneiform for Linux 1.0.0 and hOCR to PDF converter, 
version 0.7.4 (should be the most current version) I get a sandvich pdf that 
looks nice until I select text.

See the sample 5AADFEE1-0000.* files in the attachment and the result.pdf.
The effect is shown in screen087.png

For another file (Test10pages.pdf) the effect is either worse - basically I 
cannot really select any more text to copy because I only can guess where to 
move with the mouse.

It looks like that the font size in the HTML is somehow not correct - I am not 
an expert, but this link might help you:
http://www.emdpi.com/fontsize.html



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