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jlab / rust-debruijn
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Repo Added 02 Apr 2025 10:06AM UTC
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  • feat/phred-scores
  • feature/compress_edge_mults
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04 May 2026 09:41AM UTC coverage: 88.239% (+1.0%) from 87.212%
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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`

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

Relevant lines Covered
Build:
Build:
10186 RELEVANT LINES 8988 COVERED LINES
4140519.27 HITS PER LINE
Source Files on master
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  • Changed 12
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Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
25312024362 master 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 ... push 04 May 2026 09:43AM UTC web-flow github
88.24
19666544191 master Merge pull request #36 from jlab/dev Optional `Exts` in `Reads`, memory limit fixes push 25 Nov 2025 10:37AM UTC web-flow github
87.21
17157087581 master Merge pull request #30 from jlab/mergre_map_transcripts Transcript Mapping - new `IDEMData` summarizer: can hold (gene) IDs and edge coverage - new option to translate (group) IDs into ID-groups (orthogroups) when printing node info - new `Debrui... push 22 Aug 2025 01:51PM UTC web-flow github
87.37
17153954075 master Merge pull request #28 from jlab/merge_filter_edges - all k-mer sizes up to 64 - new method `DebruijnGraph::to_dot_with_paths`: prints to dot while highlighting a path - new method `DebruijnGraph::iter_edges`: iterates over all edges of the grap... push 22 Aug 2025 11:24AM UTC web-flow github
87.37
15710337174 master Merge pull request #24 from jlab/dev More summarizers, `id4b` feature new summarizers: - `TagsData`: only 1-bit enocoded tags - `IDData`: only IDs - `IDTagsCountsData` and `IDTagsCountsPEMData`: both IDs and tags + Counts etc. new `id4b` featu... push 17 Jun 2025 02:40PM UTC web-flow github
87.29
14991022630 master Merge pull request #18 from jlab/dev `EdgeMult` compression - add `EdgeMult` compatibility with graph compression - remove parallel compression methods push 13 May 2025 07:44AM UTC web-flow github
85.95
14642889194 master Merge pull request #15 from jlab/dev Paired & Stranded reads paired: - `ReadsPaired` stuct to store up to three `Reads` in and how they are paired - methods to iterate over the reads stranded: - `Stranded` enum stored in `Reads` stuct - adapt... push 24 Apr 2025 01:31PM UTC web-flow github
84.79
14356925917 master Merge pull request #12 from jlab/dev New DOT edge format - customizable format for `dot` edges - `Colors` (from `dbg`) to calculate variable colors - default methods for formatting edges and nodes: `Node::edge_dot_default` and `node_dot_default`... push 09 Apr 2025 12:19PM UTC web-flow github
84.27
14265292510 master Merge pull request #7 from jlab/dev New `Reads` struct and revamped summarizers - new `reads::Reads` struct for compact reads storage - new handling of ambiguous bases - move summarize methods to `SummaryData` - add new functionality to `Summary... push 04 Apr 2025 12:27PM UTC web-flow github
82.58
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