jlab / rust-debruijn / 26744360352

88%

Build Type

push

github

Committed by web-flow

Commit Message

Merge pull request #43 from jlab/dev

Memory fixes, extended error removal methods, add `EdgeMap`

- increase memory efficiency of `BaseGraph`
- remove disconnection check in k-mer quality edge filter during graph construction
    - the filter now excludes all k-mer occurrences with a low quality, even if this removes the k-mer from the graph or disconnects it on one side
 -  implement default methods in `SummaryData` and remove them from the trait implementations
 - add `DebruinGraph::map_transcripts_to_edges` which maps sequences from a FASTA reference to the edges of a graph instead of the nodes
 - add `DebruijnGraph::remove_lc_paths` which works similar to `remove_lq_paths` but uses the edge coverage instead of the node quality
 - adapt error removal and reference mapping algorithms to be able to handle unstranded graphs

Coverage Stats

774 of 855 new or added lines in 6 files covered. (90.53%)

8 existing lines in 2 files now uncovered.

9312 of 10529 relevant lines covered (88.44%)

3818387.85 hits per line