v0.10.0

[0.10.0]

• Large cleanup of internal and public API.
• Runtime dependencies removed (byteorder, num_cpus, auto_impl, and memchr).
• Deprecated items removed from the public API.
• Documentation overhaul: docs now center on CBQ as the recommended variant (VBQ is documented as superseded), examples use CBQ throughout, and docstrings are heavily simplified across the crate.

Removed

• bq::StreamWriter / bq::StreamWriterBuilder
  • pure delegating wrappers; compose bq::WriterBuilder with std::io::BufWriter instead (see the network_streaming example).
• Deprecated write_record / write_paired_record on the bq and vbq writers
  • use push(SequencingRecord).
• bq::Encoder from the public API
  • bq and vbq now share one internal encoder;
  • sequence-length validation happens in bq::Writer::push.
• vbq::BlockIndex::from_vbq
  • indexes are embedded in VBQ files - removing this holdover from way back when;
  • use MmapReader::load_index.
• Redundant header constructors
  • bq::FileHeader::{new, new_extended, set_bitsize} and vbq::FileHeader::{new, with_capacity, set_bitsize};
  • use the FileHeaderBuilders.
• Never-constructed error variants
  • the five WriteError flag-mismatch variants and CbqError::MissingSequenceOnSequencingRecord;
  • BuilderError folds into HeaderError::MissingSequenceLength and FastxEncodingError into WriteError.
• &R / &mut R impls of BinseqRecord
  • the auto_impl dependency is dropped and nothing used the reference impls;
  • pass records by value (they are already references anyways).
• Dead accessors throughout (RefRecord::{config, set_id}, cbq writer usage / bytes_written, and similar zero-caller items), plus the redundant streaming and write examples.

Changed

• SequencingRecord fields are now public and the getters are removed
• FASTX encoding now drains only completed blocks per batch and does a final drain per thread
  • CBQ blocks stay full across batches for better compression and less time under the global writer lock.
• Dependencies: byteorder replaced with std little-endian conversions (byte-identical output), num_cpus replaced with std::thread::available_parallelism, auto_impl dropped, and memchr moved to dev-dependencies.
• The paraseq feature is no longer enabled by default, reducing compile times when FASTX encoding is not needed. Enable it with features = ["paraseq"] to use encode_fastx (which remains visible on docs.rs with a feature banner).
• anyhow is now actually an optional dependency (still enabled by default; opt out with default-features = false):
  • the CBQ Elias-Fano codec is handled directly without the auto-derive from thiserror
  • fixes the optional feature which actually never compiled when disabled.
• paraseq updated 0.5 -> 0.6 (breaking for users of the paraseq feature and encode_fastx).
• Dependencies updated: bitnuc 0.5.7, rand 0.10, sucds 0.9, zstd 0.14, and thiserror 2.0.21.
• Internal simplification:
  • one shared bq/vbq encoder
  • BatchRecord wraps RefRecord
  • cbq Span replaced by Range<usize>
  • unreachable pub items demoted to pub(crate).

Fixed

• The error test module was missing #[cfg(test)], so a test-only enum compiled into release builds.
• cbq::Index::average_block_size reports 0.0 instead of NaN for files with fewer than two blocks.
• encode_fastx with single non-paired input no longer records second read's length as xlen
  • made fixed-length BQ output look paired and fail on interleaved encoding.
  • The extended length now only probes when builder is configured paired.