Module compression 

Create compressed DeBruijn graphs from uncompressed DeBruijn graphs, or a collection of disjoint DeBruijn graphs.

Structs

CheckCompress

CompressionSpec with custom check and function

ScmapCompress

Extending trait CompressionSpec for compression

SimpleCompress

Simple implementation of CompressionSpec that lets you provide that data reduction function as a closure

Traits

CompressionSpec

Customize the path-compression process. Implementing this trait lets the user control how the per-kmer data (of type D) is summarized into a per-path summary data (of type DS). It also let’s the user introduce new breaks into paths by inspecting in the per-kmer data of a proposed with join_test_kmer function.

Functions

compress_graph

Perform path-compression on a (possibly partially compressed) DeBruijn graph

compress_kmers

Take (make) a BoomHash Object and build a compressed DeBruijn graph.

compress_kmers_no_exts

Build graph from a set of kmers with unknown extensions by finding the extensions on the fly.

compress_kmers_with_hash

Take a BoomHash Object and build a compressed DeBruijn graph.

rebuild_uncompressed_graph

re-build an uncompressed graph while leaving out nodes

uncompressed_graph

build an uncompressed graph from hashed k-mers