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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

`.skm` File Format and `SkmWriter` Functionality

The Go package obikmer provides a binary writer for .skm (super-kmer) files, optimized for compact storage of DNA sequences.

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

.skm File Format and SkmWriter Functionality