  The study of genomic variation has provided key insights into the functional
role of mutations. Predominantly, studies have focused on single nucleotide
variants (SNV), which are relatively easy to detect and can be described with
rich mathematical models. However, it has been observed that genomes are highly
plastic, and that whole regions can be moved, removed or duplicated in bulk.
These structural variants (SV) have been shown to have significant impact on
the phenotype, but their study has been held back by the combinatorial
complexity of the underlying models. We describe here a general model of
structural variation that encompasses both balanced rearrangements and
arbitrary copy-numbers variants (CNV). In this model, we show that the space of
possible evolutionary histories that explain the structural differences between
any two genomes can be sampled ergodically.
