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)
1.2 KiB
SKM File Reader for Super-Kmers
This Go package provides a binary file reader (SkmReader) for .skm files, which store super-kmers — compact representations of DNA sequences using 2-bit encoding.
Core Functionality
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Binary Format Parsing: Reads structured data from
.skmfiles, where each record contains:- A 2-byte little-endian integer specifying the sequence length.
- Packed nucleotide data, where every byte encodes up to four bases (2 bits per base).
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Decoding Logic: Converts packed 2-bit codes (
00,01,10,11) to nucleotide characters using the mapping:
{ 'a', 'c', 'g', 't' }. -
Memory-Efficient Reading: Uses buffered I/O (64 KiB buffer) for fast sequential access.
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Streaming Interface:
Next()returns the next super-kmer as a struct with:Sequence: decoded nucleotide byte slice.Start,End: positional metadata (currently fixed to full length).
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Resource Management: Provides a clean
.Close()method for file handle cleanup.
Use Case
Designed for high-performance processing of large genomic datasets (e.g., in k-mer analysis or sequence indexing), where storage size and read speed are critical.