You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
This commit was created on GitHub.com and signed with GitHub’s verified signature.
Added
compress --estimate — predict the compression ratio and archive size
for a FASTQ without writing an archive. --estimate tsv emits machine-readable
output, and info/verify now accept multiple files or directories for batch
reporting.
Reference sequence coder for --max/reorder — a SPRING-style codec that
2-bit-packs the assembled global reference and entropy-codes it with a
clean-room LZMA, adopted only when it beats the raw representation.
--order shuffle renumber mode — a true SPRING-style read renumbering that
discards the input permutation, reaching SPRING-competitive ratios on datasets
where read order carries no information.
CLI run feedback — a TTY-aware progress spinner and human-readable
compress/decompress run summaries (suppressed under --quiet and when stderr
is not a terminal).
Changed
Quality coding — fqzcomp now models quality over the symbol alphabet that
actually occurs in the file rather than a fixed 0..QMAX range, shrinking the
quality stream on data with sparse quality alphabets. Byte-identical
round-trips are preserved.
Performance
Reorder merge — the overlap-merge k-mer index now uses a rolling hash with
sharding (~10% faster --max, byte-identical output), and the merge_reference vote-scatter is parallelized.
Documentation
VHS-rendered terminal demos on the docs site, refreshed benchmarks (including
an fqxv-shuffle row), and clearer positioning.