jlab / rust-debruijn
88%

DEFAULT BRANCH: master
Repo Added
Files 17
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

LAST BUILD ON BRANCH master
branch: master
CHANGE BRANCH
x

coverage: 88.239% (+1.0%) from 87.212%
25312024362

push

github

web-flow 
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
10186 RELEVANT LINES 8988 COVERED LINES
4140519.27 HITS PER LINE
Source Files on master

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 web-flow github
88.24
19666544191 master Merge pull request #36 from jlab/dev Optional `Exts` in `Reads`, memory limit fixes push 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 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 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 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 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 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 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 web-flow github
82.58
See All Builds (179)