# Changelog
## 0.35.0 - 2024-05-16
### Changed
* csi: Sync dependencies.
## 0.34.0 - 2024-05-08
### Changed
* csi: Sync dependencies.
## 0.33.0 - 2024-05-02
### Changed
* csi/io/query: Allow a generic buffered, seekable BGZF reader
(`Query::new`).
## 0.32.0 - 2024-03-28
### Changed
* csi: Sync dependencies.
## 0.31.0 - 2024-03-12
### Changed
* csi: Sync dependencies.
## 0.30.0 - 2024-01-25
### Changed
* csi: Sync dependencies.
## 0.29.0 - 2023-12-14
### Added
* csi: Readd `BinningIndex`.
This now encompasses a more generic interface to binning indices than
before, as it no longer includes access to the reference sequences. Import
`BinningIndex` if previously using `Index::min_shift`, `Index::depth`,
`Index::header`, `Index::unplaced_unmapped_record_count`, or
`Index::query`.
* csi: Move `Index` under the `binning_index` module.
* csi/binning_index/index/reference_sequence/bin: Add `Bin::add_chunk` to add
or merge a chunk.
`Bin` no longer has a builder.
* csi/io/index_reader: Add type parameter for the index.
### Changed
* csi: Raise minimum supported Rust version (MSRV) to 1.70.0.
* csi: Increase the visibility of the `reader` module.
* csi: Define `csi::Index` as `binning_index::Index<BinnedIndex>`.
* csi/binning_index: Move `Indexer` under `binning_index` module.
### Removed
* csi/binning_index/index/reference_sequence/bin: Remove `Bin::loffset`.
First record positions for each bin is now moved to the reference sequence.
* csi/binning_index/index/reference_sequence: Remove `Builder`.
Use `ReferenceSequence::update` instead.
* csi/binning_index/index/reference_sequence/bin: Remove `Builder`.
Use `Bin::add_chunk` instead.
## 0.28.0 - 2023-11-14
### Added
* csi/reader/index: Add read errors.
### Changed
* csi: Rename `aux` module ([#217]).
Windows does not allow the `aux` module to be named `aux.rs`.
[#217]: https://github.com/zaeleus/noodles/issues/217
## 0.27.0 - 2023-11-13
### Changed
* csi/async/reader: Disallow duplicate bin IDs.
### Fixed
* csi/reader: Fix column indices being off-by-one when reading a tabix
header ([#215]).
* csi/writer: Fix column indices being off-by-one when writing a tabix
header ([#215]).
* csi/writer: Fix writing the end position of a chunk ([#216]).
[#215]: https://github.com/zaeleus/noodles/issues/215
[#216]: https://github.com/zaeleus/noodles/issues/216
## 0.26.0 - 2023-10-26
### Changed
* csi/index/reference_sequence: Change bins to an ordered map ([#213]).
Bins now maintain their insertion order. While this does not directly
affect reading and in-memory usage, it does make serialization
deterministic.
[#213]: https://github.com/zaeleus/noodles/issues/213
## 0.25.1 - 2023-10-19
### Fixed
* csi/index/indexer: Fix final reference sequence count when building index.
## 0.25.0 - 2023-10-12
### Changed
* csi: Sync dependencies.
## 0.24.0 - 2023-08-31
### Changed
* csi: Sync dependencies.
## 0.23.0 - 2023-08-17
### Changed
* csi: Sync dependencies.
## 0.22.0 - 2023-07-06
### Changed
* csi: Update to indexmap 2.0.0.
## 0.21.0 - 2023-06-29
### Added
* csi/index/reference_sequence/bin: Make `Bin::max_id` and `Bin::metadata_id`
`const`.
### Changed
* csi/reader: Disallow duplicate bin IDs.
## 0.20.0 - 2023-06-15
### Changed
* csi: Sync dependencies.
## 0.19.0 - 2023-06-01
### Fixed
* csi/index/reference_sequence: Use the available linear index for the start
position of the first record in the last linear bin ([#172]).
[#172]: https://github.com/zaeleus/noodles/issues/172
## 0.18.0 - 2023-05-18
### Added
* csi/io: Add a filtered indexed records iterator (`FilterByRegion`).
This filters indexed records that intersect a given region.
* csi/io: Add an indexed records iterator (`IndexedRecords`).
This parses lines from a reader as an indexed record.
* csi/io: Add `IndexedRecord` trait to represent the components used to
index a record.
I.e., a reference sequence name, start position, and end position.
* csi/io: Add an indexed reader (`IndexedReader`).
* csi/io/query: Add `Query::indexed_records` to create an
iterator of indexed records.
### Changed
* csi/index/header: Change column indices to be 0-based.
## 0.17.0 - 2023-05-04
### Added
* csi/io: Add `Query` reader for reading the uncompressed data between all
the given chunks.
## 0.16.0 - 2023-04-27
### Changed
* csi: Sync dependencies.
## 0.15.0 - 2023-04-06
### Added
* csi/async: Add a convenience write function to write an index to a file
(`csi::r#async::write`).
* csi/index: Add an indexer (`csi::index::Indexer`) ([#157]).
* csi/index: Add `Header`.
This is the same structure as a tabix header. It was moved from
`noodles_tabix::index::Header`.
* csi/index/reference_sequence: Add a linear index
(`ReferenceSequence::linear_index`).
This is optional and may be preferred over bin linear offsets.
* csi/index/reference_sequence/builder: Build linear index.
[#157]: https://github.com/zaeleus/noodles/issues/157
### Changed
* csi/index: Replace `aux` with an optional tabix header
(`Option<csi::index::Header>`).
It isn't clear what `aux` is supposed to be used for, so noodles-csi
assumes if it's set, it's a tabix header.
* csi/index: Optimize chunks from `Index::query`.
* csi/index/reference_sequence: Increase the visibility of `Builder`.
* csi/index/reference_sequence: Change bins to a `HashMap<usize, Bin>`.
`Bin` no longer holds its bin ID.
* csi/index/reference_sequence/bin: Increase the visibility of `Builder`.
### Removed
* csi: Remove `BinningIndex`.
`csi::Index` is now the only concrete implementation of a binning index.
## 0.14.0 - 2023-03-03
### Changed
* csi: Sync dependencies.
## 0.13.0 - 2023-02-03
### Changed
* csi: Raise minimum supported Rust version (MSRV) to 1.64.0.
### Removed
* csi: Remove `BinningIndexReferenceSequence`.
This was deprecated in noodles-csi 0.4.0. Use
`noodles_csi::binning_index::ReferenceSequenceExt` instead.
* csi/index: Remove `Index::unmapped_read_count`.
This was deprecated in noodles-csi 0.2.0. Use
`Index::unplaced_unmapped_record_count` instead.
* csi/index/builder: Remove `Index::set_n_no_coor`.
This was deprecated in noodles-csi 0.2.0. Use
`Builder::set_unplaced_unmapped_record_count` instead.
## 0.12.0 - 2022-11-18
### Changed
* csi: Sync dependencies.
## 0.11.0 - 2022-10-28
### Changed
* csi: Sync dependencies.
## 0.10.0 - 2022-10-20
### Changed
* csi: Sync dependencies.
## 0.9.1 - 2022-09-29
### Fixed
* csi: Sync dependencies.
## 0.9.0 - 2022-08-16
### Changed
* csi: Raise minimum supported Rust version (MSRV) to 1.57.0.
## 0.8.0 - 2022-07-05
### Added
* csi/index/reference_sequence: Add finding the minimum start virtual
position for a bin (`ReferenceSequence::min_offset`).
* csi/index/reference_sequence/bin/chunk: Implement
`From<Range<bgzf::VirtualPosition>>` for `Chunk`.
### Fixed
* csi/index/reference_sequence: Fix finding the start position of the first
record in the last linear bin.
The bins are not necessarily sorted.
## 0.7.0 - 2022-06-08
### Changed
* csi/binning_index: Change generic reference sequence type to an associated
type.
* csi/binning_index: Change query interval to `Into<Interval>`.
* csi/index/reference_sequence/bin: Change bin ID to a `usize`.
## 0.6.0 - 2022-03-29
### Changed
* csi/binning_index: Change interval bounds to `Position`.
* csi/index: Change `min_shift` and `depth` to a `u8`.
* csi/index/reference_sequence: `ReferenceSequence::query` returns an
`io::Error` instead of `QueryError`.
### Fixed
* csi/index/reference_sequence: Ensure the start position is not out of range
for a query.
## 0.5.1 - 2022-03-02
### Fixed
* csi: Sync dependencies.
## 0.5.0 - 2022-02-17
### Added
* csi: Set minimum supported Rust version (MSRV) to 1.56.0 in package
manifest.
## 0.4.3 - 2022-01-27
### Fixed
* csi: Sync dependencies.
## 0.4.2 - 2021-12-02
### Fixed
* csi: Require tokio's `fs` feature as a dependency ([#62]).
[#62]: https://github.com/zaeleus/noodles/issues/62
## 0.4.1 - 2021-11-18
### Fixed
* csi: Sync dependencies.
## 0.4.0 - 2021-11-11
### Changed
* csi: Update to Rust 2021.
### Deprecated
* csi/binning_index: Rename `csi::BinningIndexReferenceSequence` to
`csi::binning_index::ReferenceSequenceExt`.
## 0.3.0 - 2021-08-19
### Added
* csi/async: Add async reader (`csi::AsyncReader`).
* csi/async: Add async writer (`csi::AsyncWriter`).
Async I/O can be enabled with the `async` feature.
## 0.2.2 - 2021-08-11
### Fixed
* csi: Sync dependencies.
## 0.2.1 - 2021-07-30
### Fixed
* csi/reader: Return I/O errors when failing to read `n_no_coor`.
This previously ignored all I/O errors but now only catches
`UnexpectedEof`.
## 0.2.0 - 2021-07-21
### Added
* csi: Add convenience function to write an entire index to a file:
`csi::write`.
* csi/binning_index: Added chunk merging functions for chunk list reduction
(`noodles_csi::binning_index::{merge_chunks, optimize_chunks}`).
Chunks are merged when they overlap and can be filtered by a minimum
offset.
* csi/binning_index: Added `BinningIndex` and `BinningIndexReferenceSequence`
traits to define shared behavior among binning index formats.
* csi/binning_index: Added `first_record_in_last_linear_bin_start_position`.
This is the closest position to the unplaced, unmapped records, if any,
that is available in an index.
* csi/index: Implemented `BinningIndex` for `Index`.
* csi/index: Added `query` method to find chunks that intersect the given
region.
* csi/index/reference_sequence: Implemented `BinningIndexReferenceSequence`
for `ReferenceSequence`.
### Deprecated
* csi/index: Deprecated `Index::unmapped_read_count`.
Use `unplaced_unmapped_record_count` instead.
* csi/index/builder: Deprecated `Builder::set_n_no_coor`.
Use `set_unplaced_unmapped_record_count` instead.
### Fixed
* csi: Fixed documentation link in package manifest ([#31]).
[#31]: https://github.com/zaeleus/noodles/issues/31
## 0.1.0 - 2021-07-14
* csi: Initial release.