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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)
25 lines
1.3 KiB
Markdown
25 lines
1.3 KiB
Markdown
# `.skm` File Format and `SkmWriter` Functionality
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The Go package `obikmer` provides a binary writer for `.skm` (super-kmer) files, optimized for compact storage of DNA sequences.
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- **Purpose**: Efficiently serialize *super-kmers* (long k-mers) into a binary format.
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- **Format per super-kmer**:
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- `len: uint16 LE` — length of the sequence in bases (little-endian, 2 bytes).
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- `data: ⌈len/4⌉ bytes` — nucleotide sequence encoded as **2 bits per base**, packed tightly.
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- **Encoding scheme**:
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- `A → 00`, `C → 01`, `G → 10`, `T → 11`.
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- Padding: trailing bits in the final byte are zeroed if `len % 4 ≠ 0`.
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- **Implementation details**:
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- Uses buffered I/O (`bufio.Writer` with 64 KiB buffer) for performance.
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- `NewSkmWriter(path)` opens/creates the file and returns a writer instance.
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- `Write(sk SuperKmer)` encodes sequence length, then packs bases using a lookup (`__single_base_code__[seq[pos]&31]`).
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- `Close()` flushes buffers and closes the file handle.
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- **Use case**: Ideal for high-throughput genomic preprocessing (e.g., indexing, sketching), where space and I/O speed matter.
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- **Assumptions**: `SuperKmer` type exposes a `.Sequence []byte`; bases are ASCII (`A,C,G,T,a,c,g,t`) — `&31` normalizes to lowercase index.
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- **Efficiency**: 4× compression vs. ASCII (1 byte/base → ~0.25 bytes/base), minimal overhead.
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