Module contig_compression 

Contig compression with inline segmentation

This module implements C++ AGC’s compress_contig and add_segment logic for inline segmentation during compression.

See docs/INLINE_SEGMENTATION_PATTERN.md for detailed C++ AGC analysis.

Structs

CompressionContext

Shared state for compression (passed from worker threads)

SegmentPart

Segment part for inline buffering

Constants

MISSING_KMER

Missing k-mer marker (matches C++ AGC’s kmer_t(-1) = u64::MAX)

Functions

compress_contig

Compress a contig with inline segmentation

Type Aliases

Contig

Contig type (vector of nucleotides in numeric encoding)