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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.11.0]

Changed

  • bump slow5lib submodule to v1.1.0
  • bump slow5lib-sys to v0.9.0

Fixed

  • Switch from deprecated bindgen::Builder rustfmt_bindings method to formatter

[0.10.0] - 2022-12-27

Added

  • reader: AuxEnumLabelIter and FileReader::iter_aux_enum_label for iterating through the labels for an enum auxiliary field
  • reader: AttrKeyIter and FileReader::iter_attr_keys for iterating through the keys of all the attributes
  • auxiliary: EnumField type for getting/setting enum values for auxiliary fields
  • parallel: Add Send impl for FileReader, RecordIter, and Record
  • parallel: parallel read example for reading records in parallel with rayon ParallelBridge
  • field: Add impl Vec<B> for B: Into<Vec<u8>> as a convience for the FieldType::Enum variant
  • errors: Additional errors for dealing with auxiliary setting
  • serde: Add Serialize implementation for Record and optional serde dependency

Changed

  • record: RecordIter now holds a FileReader instead of a *mut slow5_file
  • deps: zstd is now an optional dependency, enabled by default but can be disabled by setting default-features = false
  • deps: bindgen dependency upgraded to 0.63
  • aux: AuxFieldSetExt is pub
  • write: WriteOptions::aux can now add enums
  • record: Record::get_aux_field now takes a impl Into<Vec<u8>> which should make the turbofish syntax less awkward

Removed

  • aux: Removed the to_slow5_t required method on AuxField since it wasn't necessary and making dealing with enums harder

Fixed

  • mem: Fixed potential memory leaks during error paths

[0.9.0] - 2022-12-10

Added

  • auxiliary: Added support for string (char *) and array auxiliary fields.
  • reader + writer: Error for invalid file path based on the file extension.
  • compression: File*::record_compression + File*::signal_compression to check what compression was used.
  • all: Debug implementations for public types
  • header: HeaderExt for using File* as a Header
  • record: AuxFieldSetExt trait for specifying which types are allowed to be used to set auxiliary fields.

Changed

  • writer: FileWriter returns Err(Slow5Error::Slow5CompressionError) if compression options are set for SLOW5 file output
  • record: Record::set_aux_field value must implement AuxFieldSetExt instead of AuxField
  • header: aux_names_iter will always return and for SLOW5 files with no auxiliary fields, it just returns an empty iterator

Fixed

  • record: Fixed bug in Record::set_aux_field where no error would occur but value would not get written to file. Fixed by extending lifetime of String used to set the aux_field and storing it in FileWriter.

[0.8.1] - 2022-12-03

Fixed

  • Fixed link to documentation on crates.io

[0.8.0] - 2022-12-03

Added

  • aux: AuxField trait map Rust types and C types that can represent auxiliary fields, currently only supports primitive data types
  • writer: WriteOptions is a builder for FileWriter with auxiliary fields, attributes, and compression
  • writer: Added FileWriter::header to get access to SLOW5 header
  • record: Added Record::get_aux_field and Record::set_aux_field for accessing Record auxiliary fields
  • record: Added PicoAmpsSignalIter and RawSignalIter for signal data iteration
  • reader: Added ReadIdIter and FileReader::read_id_iter to iterate over all read ids in a SLOW5 file
  • headers: Added AuxNamesIter and Header::aux_names_iter for going over auxiliary name keys
  • docs: Fill out documentation for more items
  • api: RecordPointer wraps the raw pointer and try to avoid leaking API
  • examples: New example slow5 and blow5 files for testing and examples
  • examples: auxiliary_field.rs to model slow5lib example

Changed

  • record: RecordIter returns a Record
  • sys: slowlib-sys now compiles with SIMD based on architecture, or disables it entirely. So it should now compile on more archtectures.

Deprecated

Removed

  • writer: FileWriter::write_record remove, didn't add much and overlaps with add_record
  • record: picoamps argument to some of the Record/RecordView
  • record: remove SignalIterExt and combine with RecordExt
  • record: remove SignalIter and replace with Raw and PicoAmp version
  • header: remove HeaderView since all header attributes will be initialized at the beginning and no reason to mutate it afterwards.
  • record: RecordBuilder::builder(), now moved to Record::builder to follow builder pattern
  • record: RecordView removed because it was only used for iteration but ended creating a use-after-free bug so allocation is required anyways

Fixed

  • bug: use-after-free bug in RecordIter removed