obitools4/autodoc/docmd/pkg/obikmer/superkmer_iter.md

Super K-mers Extraction Module (obikmer)

This Go package provides efficient tools for extracting super k-mers from DNA sequences using minimizer-based sliding windows. Super k-mers are maximal contiguous subsequences sharing the same minimal canonical minimizer in a window of size k.

Core Functionality

• IterSuperKmers(seq, k, m)
  Returns an iterator over SuperKmer structs. Each struct contains:

  • Start, End: genomic positions of the super k-mer in the original sequence
  • Minimizer: canonical minimizer value (uint64) for that segment
  • Sequence: the actual DNA subsequence

• SuperKmer.ToBioSequence(...)
  Converts a raw SuperKmer into an enriched obiseq.BioSequence, embedding metadata:

  • ID: {parentID}_superkmer_{start}_{end}
  • Attributes: minimizer sequence (minimizer_seq), value, k, m, positions, and parent ID

• SuperKmerWorker(k, m)
  A SeqWorker adapter for pipeline integration (e.g., with obiiter). Processes a full BioSequence and returns all extracted super k-mers as a slice of BioSequences.

Algorithm Highlights

• Uses canonical minimizers (forward/reverse-complement minimum) to ensure strand-invariance
• Maintains a monotonic deque for efficient sliding-window minimizer tracking (O(n) time complexity)
• Supports DNA bases A/C/G/T/U case-insensitively via bitmasking (seq[i] & 31)
• Enforces parameter constraints: 1 ≤ m < k ≤ 31, sequence length ≥ k

Use Cases

• Read partitioning in metagenomics (e.g., for error correction or clustering)
• Efficient k-mer space segmentation without storing all individual kmers
• Integration into modular bioinformatics pipelines via SeqWorker interface