CSEM (Chung et al. 2011) uses an expectation-maximization algorithm to probabilistically reassign multi-mapping reads across the genome, producing a BAM in which multi-reads are allocated proportionally to local enrichment. Reference: Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, et al. Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. PLoS Comput Biol. 2011;7:e1002111.