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Type 1 conflicts not marked due to unset pos attribute #26

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@julunt

It occurred to me that type 1 conflicts don't actually get marked in the current implementation, despite there being a function call that should be doing this.

The problem is that when mark_type_1_conflicts gets called here, the pos attribute of the node weights is not yet set, so it is still 0. The reset_alignment function, which to my knowledge is the only function that actually sets pos, is only called afterwards.

Type 1 conflicts not being marked does affect node positioning, so this is actually a problem.

Calling reset_alignment right before the call to mark_type_1_conflicts seems to fix the issue and should be safe as far as I can tell.

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