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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)
1.4 KiB
1.4 KiB
SKM File Format Specification
This Go package implements a binary format for storing super-kmers—compact representations of DNA sequences used in bioinformatics. The tests validate reading/writing, padding behavior, and file size correctness.
Core Functionalities
- SuperKmer Structure: Each super-kmer stores a DNA sequence (as bytes), likely padded to 4-base boundaries for efficient storage.
- SkmWriter: Serializes super-kmers into a binary file. Each entry writes:
- A 2-byte little-endian length (number of bases),
- Then
ceil(length/4)bytes encoding nucleotides in 2 bits each (A=0, C=1, G=2, T=3).
- SkmReader: Parses the binary format back into memory. Returns
(SuperKmer, bool)viaNext(), with EOF signaled byok = false. - Case Handling: Writes preserve original case; reads normalize to lowercase (via
| 0x20in tests), ensuring robust comparison.
Test Coverage
- Round-trip integrity: Verifies exact sequence recovery after write/read.
- Empty file handling: Confirms reader returns
ok = falseimmediately on empty files. - Variable-length padding: Validates correct encoding/decoding for sequences of length 1–5.
- Size validation: Confirms file size =
2 + ceil(L/4)bytes for a sequence of length L.
Use Case
Efficient, lossless storage and retrieval of super-kmers for downstream genomic analysis (e.g., assembly or alignment acceleration).