When counting lines for a window with the linemarker displayed in it, it will count the lines including the linemarker.

There's no way to tell wether the linemarker is either turned on or off, so you'll never know precisely how many lines there are in a certain window with a possible linemarker enabled.

Command:
$line(windowname,0)

Another effect of this is that it will return nothing when there is a linenumber specified where a linemaker has it's position..

Command:
$line(windowname,1)

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Using mIRC 6.16