Package org.broadinstitute.hellbender.tools.sv.cluster
package org.broadinstitute.hellbender.tools.sv.cluster
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ClassDescriptionCNV defragmenter for when the intervals used for coverage collection are available.Class for collapsing a collection of similar
SVCallRecord
objects, such as clusters produced byCanonicalSVLinkage
, into a single representative call.Define strategies for collapsing alt alleles with different subtypes.Define strategies for collapsing variant intervals.CanonicalSVLinkage<T extends SVCallRecord>Main class for SV clustering.Stores clustering parameters for different combinations of supporting algorithm types (depth-only/depth-only, depth-only/PESR, and PESR/PESR)Clustering engine class for defragmenting depth-based DEL/DUP calls, such as those produced byGermlineCNVCaller
.Base class for clustering items that possess start/end genomic coordinates.Available clustering algorithmsArguments for use withSVClusterEngine
.Some useful functions for creating different kinds ofSVClusterEngine
.SVClusterLinkage<T extends SVLocatable>