jlab / rust-debruijn / 25312024362

88%

Build Type

push

github

Committed by web-flow

Commit Message

Merge pull request #40 from jlab/dev

Utilize PHRED-scores for error removal, add 3D json compatibility

### Utilize PHRED-scores for error removal

- the quality scores from the sequencing reads can be stored in a `Reads`
- the scores are binned into four categories in accordance with [this](https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/novaseq-hiseq-q30-app-note-770-2017-010.pdf) document on Illumina NovaSeq Quality Scores.
- it can be used to assess the validity of each k-mer during graph construction
  - option 1: only include k-mers which have occurred with all bases having at least a specific quality
  - option 2: only include edges of k-mer occurrences with all bases having at least a specific quality, unless this would disconnect the k-mer on one or both sides
- the quality scores can also be saved in the graph nodes by using the `SummaryData` implementations `IDMapEMQualityData`,`SumMapEMQualityData`, or `TagsCountsPEMQualityData` - this can be used to apply two error removal algorithms to the graph
  - `DebruijnGraph::remove_lq_ladders_tips` will remove any ladders (bubbles) and tips which are not supported by good quality k-mers. 
  - `DebruijnGraph::remove_lq_splits` is more radical and will identify nodes at which the path splits into a good and bad quality path, or at which a good and bad quality path merge, and remove the connection to the bad quality path

### 3D JSON compatibility

- a `DebruijnGraph` can now be saved to a JSON file compatible with [https://github.com/vasturiano/3d-force-graph](https://github.com/vasturiano/3d-force-graph)
- default functions for node and edge format, which include all node information, are available: `Node::node_json_default` and `Node::edge_json_default`

Coverage Stats

1573 of 1714 new or added lines in 9 files covered. (91.77%)

14 existing lines in 4 files now uncovered.

8988 of 10186 relevant lines covered (88.24%)

4140519.27 hits per line