Sub-package Documentation

The cluster sub-package is responsible for merging variants coming from different inputs (i.e. different tools).

Types of Output Files

expected name/suffix	file type/format	content
`cluster_assignment.tab`	text/tabbed
`uninformative_clusters.txt`	text	list of cluster ids that were dropped by annotation proximity filter
`clusters.bed`	bed	cluster positions
`cluster-*.tab`	text/tabbed	computed clusters

Collapse any duplicate breakpoint pairs
Split breakpoint pairs by type
Cluster breakpoint pairs by distance (within a type)
- Create a graph representation of the distances between pairs
- Find cliques up to a given input size (cluster_clique_size)
- Hierarchically cluster the cliques (allows redundant participation)
- For each input node/pair pick the best cluster(s)
Output the clusters and the mapping to the input pairs