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Add performance optimizations
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 `SummaryData` (p-values, edge multiplicities) - `KmerSummarizer` removed
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` - fix nucleotide order in `EdgeMult`
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 - adaption of `filter_kmers` and `filter_kmers_parallel` to - keep forward reads as they are - reverse complement reverse reads - min rc unstranded reads fix: - add `DebruijnGraph::fix_edge_mults` to remove multiplicities of filtered nodes
`EdgeMult` compression - add `EdgeMult` compatibility with graph compression - remove parallel compression methods
new `IDSumData` summarizer, restructure `Colors` with `ColorMode` enum, new `serde` module new `IDSumData` summarizer - track IDs as `u16`s (e.g. gene IDs) restructure `Colors` with `ColorMode` enum - color dot nodes according to their tracked ID or their supergroup (e.g. orthogroups) - set the color mode (mentioned above + fold change + sample group) with the `ColorMode` enum new `serde` module - easy to use structs + methods for serializing and deserializing reads, k-mers, and graphs
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` feature: - previously there could be max. 65k unique IDs (stored in `u16`) - with the feature (compile flag) `id4b`, IDs are instead stored in `u32`s, raising this maximum to 4 billion
- 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 graph - new method `DebruijnGraph::filter_edges`: removes edges below certain coverage
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 `DebruijnGraph::map_transcripts` method: maps transcripts from a fasta file to a stranded & uncompressed graph - new `IDMapEMData` summarizer: can hold additional mapped IDs
Removing ladders + tips
Optional `Exts` in `Reads`, memory limit fixes
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`
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
Publish the Rust documentation for the crate on GitHub Pages
evolp
marked this pull request as ready for review
June 10, 2026 09:38
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