Crate libmatchtigs

A library containing the matchtigs algorithms. Use this to compute pathtigs (similar to simplitigs and UST-tigs), greedy matchtigs and matchtigs for arbitrary graph types.

Modules

• clib
  Bindings of our algorithms for the C language. These allow to pass the graph topology as a list of edges from a node-centric de Bruijn graph. There is only one global graph that can be controlled via the bindings, no two graphs can be created at the same time.

Structs

• EulertigAlgorithm
  The eulertigs algorithm.
• EulertigAlgorithmConfiguration
  The options for the eulertigs algorithm.
• GreedytigAlgorithm
  The greedy matchtigs algorithm.
• GreedytigAlgorithmConfiguration
  The options for the greedy matchtigs algorithm.
• MatchtigAlgorithm
  The matchtigs algorithm.
• MatchtigAlgorithmConfiguration
  The options for the matchtigs algorithm.
• PathtigAlgorithm
  The pathtig algorithm computes a heuristically small set of edge-disjoint paths, similar to simplitigs and UST-tigs. This algorithm does not alter the graph.

Enums

• HeapType
  The heap data structure used by Dijkstra’s algorithm.
• NodeWeightArrayType
  The type of the data structure to store the weight of visited nodes in Dijkstra’s algorithm.

Traits

• MatchtigEdgeData
  The edge data of the graph to compute matchtigs on has to implement this.
• TigAlgorithm
  An algorithm to compute tigs for a graph.

Functions

• write_duplication_bitvector
  Write a bitvector in ASCII format for each walk. The bitvector contains a 1 for each original kmer, and a 0 for each duplicate kmer. The bitvectors of different walks are separated by newlines.
• write_duplication_bitvector_to_file
  Convenience method for write_duplication_bitvector.