Audit the algorithmic thesis, archive contract, performance boundary, and reference shelf behind fq-compressor in one bilingual portal.
Abstract
fq-compressor is documented as a coupled system. Read ordering, block-local transforms, FQC indexing, benchmark methodology, and operational workflows are treated as one public contract.
What you can audit here
Primary repository anchors
include/fqc/, src/, and format responsibilitiesPerformance ledger
This portal does not separate headline numbers from archive semantics. Every metric is paired with the subsystem, methodology, or repository artifact that makes it auditable.
Open methodology3.97x
Compression ratio is presented as a bounded result, not as a floating claim detached from dataset scope.
11.9 MB/s
Compression speed is interpreted through the pipeline, chunking, and backpressure design, not as an isolated stopwatch number.
62.3 MB/s
Decode speed stays in scope because random access is only useful if retrieval remains practical under real archive workflows.
O(1)
Indexed lookup is treated as a first-class contract. The format and block map are part of the public thesis, not an implementation footnote.
System blueprint
fq-compressor is easier to audit when each phase has a clear boundary: ingest, analysis, block transforms, archive materialization, and selective retrieval.
Open system design01
FASTQ plus compressed FASTQ streams enter through parser and stream adapters.
io/fastq_parser + io/compressed_stream
02
Global statistics establish reorder intent, chunk sizing, and memory discipline.
algo/global_analyzer + common/memory_budget
03
Block-local transforms split sequence, ID, and quality responsibilities across dedicated codecs.
algo/block_compressor + quality/id streams
04
FQC writes blocks, checksums, reorder metadata, and the lookup structures needed later.
format/fqc_writer + format/index tables
05
Readers can verify, range decode, or restore original order without replaying the whole archive.
format/fqc_reader + pipeline/decompressor
The block is the smallest unit that still carries compression leverage, checksum scope, and direct lookup.
Checksums and verify flows live at the archive boundary, which keeps retrieval semantics inspectable.
Read pipeline for concurrency and flow control, then format and random access for the archive contract.
Algorithms
The whitepaper lane explains why fq-compressor splits read ordering, consensus-style sequence reduction, and quality modeling into distinct but cooperating stages.
Evidence
The benchmark lane is intentionally conservative. It shows what the repository can prove today, not every future claim the project may eventually support.
References
The reference shelf ties fq-compressor back to SPRING [R1], fqzcomp [R2], HARC [C2], NanoSpring [R3], and repository-local evidence anchors.
Reading tracks
Start with algorithms, then verify every public claim against the evidence contract.
Stay in operations when the immediate goal is to install, run, verify, or spot-check real outputs.
Read the system blueprint with contribution guidance open beside it so architectural boundaries stay visible during edits.
Use the reference shelf for papers, comparator repositories, and closeout-mode evolution notes.
Citation apparatus
Closest paper-level frame for assembly-based compression and reversible reordering.
Quality-value coding reference for stream-specific trade-offs.
Long-read comparator that clarifies what fq-compressor is not tuned for first.
Upstream reference for ordering plus consensus-and-delta reasoning.
FASTQ-specialized comparator for architecture and scope choices.
Compact quality model used as a pressure test for stream design.
Tracked machine-readable and narrative benchmark artifacts.
Historical research and governance material kept for reference only.
License-bounded extracted reference code used for study.