1. A non-transitory machine readable medium storing a program for displaying markers for assignment conflicts for shapes in a circuit design layout that are pre-assigned to different masks, the program comprising sets of instructions for: receiving a layer of the design layout comprising a plurality of pre-assigned shapes; identifying a set of initial search shapes from the plurality of pre-assigned shapes in a disjoint set; identifying a search path from an initial search shape, which has been identified, to a remaining pre-assigned shape in the disjoint set; performing an analysis on the layer to identify a plurality of error paths by identifying at least one hole in the layer using at least a number of links connecting shapes along a path, wherein an error path comprises the path that connects two pre-assigned shapes that exhibit an assignment conflict, the at least one hole borders and is enclosed by at least the two pre-assigned shapes and at least some links of the number of links, the two pre-assigned shapes have been preassigned to a same photomask or two different photomasks, and the at least some links of the number of links in the at least one hole connect two or more shapes in the layer; determining whether the initial search shape and the remaining pre-assigned shape connected by the search path exhibit an assignment conflict; adding the search path into the plurality of error paths; and displaying a marker for at least one error path of the plurality of error paths in order to visually aid a user to resolve assignment conflicts.