Fig. 1

MCAP resolves conflicts. The white ends of the segments represent head with respect to the original genome. The blue ends represent tail with respect to the original genome. “H” stands for head and “T” stands for tail in the current arrangement. a Two conflicting edges connecting two segments u and v. If the sample is known to be homogeneous (\(k=1\)), then the conflict is due to errors. If \(k=2\), MCAP seeks to separate two edges into two compatible arrangements as in b and c. b In the first arrangement, segment v is flipped, which makes the blue edge concordant. c In the second arrangement, u is flipped to make the red edge concordant