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https://github.com/metabarcoding/obitools4.git
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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
39 lines
1.5 KiB
Markdown
39 lines
1.5 KiB
Markdown
# KDI File Format and Writer
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The `obikmer` package implements a compact, sorted sequence storage format for 64-bit k-mers using delta encoding and sparse indexing.
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## Core Format (`.kdi`)
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- **Magic header**: `KDI\x01` (`4 bytes`) identifies the file type.
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- **Count field**: `uint64 LE`, total number of k-mers (patched at close).
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- **First value**: `uint64 LE`, the initial k-mer stored as an absolute integer.
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- **Deltas**: Subsequent values encoded via *delta-varint* (difference from previous k-mer), enabling high compression for sorted sequences.
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## Writer (`KdiWriter`)
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- **Strict ordering**: K-mers must be written in *strictly increasing order*.
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- Efficient buffering via `bufio.Writer` (64 KB buffer).
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- Internally tracks:
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- Current k-mer count,
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- Previous value (for delta computation),
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- Bytes written in data section.
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- **Sparse indexing**: Every `defaultKdxStride` k-mers, an entry is recorded in memory for random access.
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## Companion Index (`.kdx`)
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- Written automatically on `Close()` if indexing entries exist.
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- Stores `(kmer, file_offset)` pairs for fast seek-to-position lookups (e.g., binary search on k-mer range).
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- Enables efficient random access without full file scan.
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## Usage Pattern
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```go
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w, _ := obikmer.NewKdiWriter("data.kdi")
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for _, kmer := range sortedKMers {
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w.Write(kmer)
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}
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w.Close() // finalizes header, writes .kdx index
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```
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The format is optimized for memory-efficient storage and fast retrieval of sorted uint64 k-mers in genomic or sequence analysis pipelines.
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