Struct SharedCompressorState 

pub struct SharedCompressorState {

    pub processed_bases: AtomicUsize,
    pub processed_samples: AtomicUsize,
    pub raw_contigs: Mutex<Vec<(String, String, Vec<u8>)>>,
    pub verbosity: usize,
    pub buffered_segments: Arc<Mutex<BufferedSegments>>,
    pub splitters: Arc<Mutex<AHashSet<u64>>>,
    pub bloom_splitters: Arc<Mutex<BloomFilter>>,
    pub vv_splitters: Mutex<Vec<Vec<u64>>>,
    pub v_candidate_kmers: Vec<u64>,
    pub v_duplicated_kmers: Vec<u64>,
    pub kmer_length: usize,
    pub adaptive_mode: bool,
    pub map_segments: Arc<Mutex<AHashMap<(u64, u64), u32>>>,
    pub map_segments_terminators: Arc<Mutex<AHashMap<u64, Vec<u64>>>>,
    pub concatenated_genomes: bool,
    pub no_segments: Arc<Mutex<u32>>,
    pub no_raw_groups: u32,
    pub archive: Option<Arc<Mutex<Archive>>>,
    pub v_segments: Arc<Mutex<Vec<Option<SegmentGroup>>>>,
    pub collection: Option<Arc<Mutex<CollectionV3>>>,
    pub aux_queue: Arc<BoundedPriorityQueue<Task>>,
    pub working_queue: Mutex<Arc<BoundedPriorityQueue<Task>>>,
}

Shared state accessible to all worker threads

This matches C++ AGC’s shared variables captured by lambda (agc_compressor.cpp:1099):

• Atomic counters (processed_bases, processed_samples)
• Mutexes for shared collections (v_raw_contigs, vv_fallback_minimizers, etc.)
• Archive writer, collection descriptor, etc.

Fields

processed_bases: AtomicUsize

Total bases processed (for progress tracking)

processed_samples: AtomicUsize

Number of samples processed (for progress tracking)

raw_contigs: Mutex<Vec<(String, String, Vec<u8>)>>

Contigs that failed to compress well (need adaptive splitters) Matches C++ AGC’s v_raw_contigs (protected by mtx_raw_contigs)

verbosity: usize

Verbosity level (0 = quiet, 1 = normal, 2 = verbose)

buffered_segments: Arc<Mutex<BufferedSegments>>

Buffered segments (KNOWN + NEW) Matches C++ AGC’s CBufferedSegPart buffered_seg_part

splitters: Arc<Mutex<AHashSet<u64>>>

Splitter k-mers (exact set) Matches C++ AGC’s hs_splitters

bloom_splitters: Arc<Mutex<BloomFilter>>

Bloom filter for splitters (fast probabilistic check) Matches C++ AGC’s bloom_splitters

vv_splitters: Mutex<Vec<Vec<u64>>>

Per-thread vectors for accumulating new splitters (adaptive mode) Matches C++ AGC’s vv_splitters (agc_compressor.h:721) Each worker thread accumulates splitters, then merges at barrier

v_candidate_kmers: Vec<u64>

Reference genome singleton k-mers (for adaptive mode exclusion) Matches C++ AGC’s v_candidate_kmers (agc_compressor.h:708) Sorted for efficient set_difference operations

v_duplicated_kmers: Vec<u64>

Reference genome duplicated k-mers (for adaptive mode exclusion) Matches C++ AGC’s v_duplicated_kmers (agc_compressor.h:710) Sorted for efficient set_difference operations

kmer_length: usize

K-mer length for segmentation

adaptive_mode: bool

Adaptive compression mode (find new splitters for hard contigs)

map_segments: Arc<Mutex<AHashMap<(u64, u64), u32>>>

Map: (kmer1, kmer2) → group_id Matches C++ AGC’s map_segments Lower group_id wins when same (k1, k2) pair (earlier samples are reference)

map_segments_terminators: Arc<Mutex<AHashMap<u64, Vec<u64>>>>

Map: kmer → Vec (sorted terminators) Matches C++ AGC’s map_segments_terminators Used for split detection: find shared terminators between k1 and k2

concatenated_genomes: bool

Concatenated genomes mode (treat all contigs as one sample)

no_segments: Arc<Mutex<u32>>

Total number of segment groups (assigned group IDs) Matches C++ AGC’s no_segments

no_raw_groups: u32

Number of raw groups (groups without LZ encoding) Matches C++ AGC’s no_raw_groups

archive: Option<Arc<Mutex<Archive>>>

Archive writer for segment output Matches C++ AGC’s out_archive

v_segments: Arc<Mutex<Vec<Option<SegmentGroup>>>>

Segment groups indexed by group_id Matches C++ AGC’s v_segments (vector<CSegment*>) Lazily created when first segment arrives for that group

collection: Option<Arc<Mutex<CollectionV3>>>

Collection metadata for samples/contigs/segments Matches C++ AGC’s collection_desc

aux_queue: Arc<BoundedPriorityQueue<Task>>

Auxiliary queue for adaptive mode (re-enqueue hard contigs) Matches C++ AGC’s pq_contigs_desc_aux

working_queue: Mutex<Arc<BoundedPriorityQueue<Task>>>

Working queue pointer (switches between main and aux) Matches C++ AGC’s pq_contigs_desc_working

Implementations

impl SharedCompressorState

pub fn new( verbosity: usize, kmer_length: usize, adaptive_mode: bool, concatenated_genomes: bool, no_raw_groups: u32, main_queue: Arc<BoundedPriorityQueue<Task>>, ) -> Self

Create new shared state