# Changelog
## 0.54.0 - 2024-05-16
### Changed
* bcf/record/samples: Add lookup by sample name (`Samples::get`).
## 0.53.0 - 2024-05-08
### Changed
* bcf: Sync dependencies.
## 0.52.0 - 2024-05-02
### Removed
* bcf/io/reader: Remove `Reader::virtual_position` and `Reader::seek`.
Use the inner reader instead.
## 0.51.0 - 2024-04-22
### Added
* bcf/record/samples: Implement series selector (`Samples::select`).
### Fixed
* bcf/io/reader/record: Return EOF when site length signals EOF ([#255]).
[#255]: https://github.com/zaeleus/noodles/issues/255
## 0.50.0 - 2024-04-11
### Changed
* bcf/io/reader/record: Disallow partial site lengths.
A partial site length previously would return EOF. This is now more
strict, requiring a complete site length or EOF.
## 0.49.0 - 2024-04-04
### Added
* bcf/async/io: Add async writer (`r#async::io::Writer`).
* bcf/record: Add reference sequence name getter
(`Record::reference_sequence_name`).
* bcf/record: Add `Samples` wrapper.
This allows reading of the samples without converting to
`vcf::variant::record_buf::Samples`.
### Changed
* bcf: Move readers (`Reader` and `IndexedReader`) to writer (`Writer`) to
`io` module.
* bcf: Move lazy record to record.
Use `bcf::Record` instead of `bcf::lazy::Record`.
* bcf/async/io/reader: Change `Reader::read_header` to return a parsed header
(`vcf::Header`).
This no longer returns a raw string. String maps are also parsed and
attached to the reader. Use `Reader::string_maps` to get a reference to
the string maps.
* bcf/io/reader: Rename record to record buf.
This changes the following:
* `Reader::read_record` => `Reader::read_record_buf`,
* `Reader::records` => `Reader::record_bufs`,
* `Reader::read_lazy_record` => `Reader::read_record`, and
* `Reader::lazy_records` => `Reader::records`.
* bcf/io/reader: Return an iterator over `bcf::Record` for queries
(`Reader::query`).
* bcf/record: Rename chromosome to reference sequence name, position to
variant start, and genotypes to samples.
* bcf/record :Increase the visibilities of the bases methods
(`Record::reference_bases` and `Record::alternate_bases`).
### Removed
* bcf/async/io/reader: Remove `Reader::read_file_format`.
`Reader::read_header` now includes checking the magic number and reading
the file format version.
* bcf/header: Remove `StringMaps`.
This is moved to noodles-vcf.
* bcf/record: Remove `Record::try_into_vcf_record`.
Use `vcf::variant::RecordBuf::try_from_variant_record` instead.
## 0.48.0 - 2024-03-28
### Changed
* bcf: Sync dependencies.
## 0.47.0 - 2024-03-12
### Changed
* bcf: Sync dependencies.
## 0.46.0 - 2024-01-25
### Changed
* bcf: Sync dependencies.
## 0.45.0 - 2023-12-14
### Added
* bcf/indexed_reader: Add index getter (`IndexedReader::index`).
* bcf/reader/builder: Add `Builder::build_from_reader`.
* bcf/reader/builder: Add a compression method setter
(`Builder::set_compression_method`).
This allows the compression method to be overridden using
`bcf::io::CompressionMethod`, instead of assuming the input is
always bgzip-compressed.
Change instantiations of `bcf::reader::Builder` to
`bcf::reader::Builder::default()`.
* bcf/writer: Add builder (`bcf::writer::Builder`).
### Changed
* bcf: Raise minimum supported Rust version (MSRV) to 1.70.0.
* bcf: Increase the visibility of the `writer` module.
* bcf/async/reader: Accept `csi::BinningIndex` for querying.
* bcf/reader: Accept `csi::BinningIndex` for querying.
## 0.44.0 - 2023-11-14
### Changed
* bcf: Sync dependencies.
## 0.43.0 - 2023-11-13
### Changed
* bcf: Sync dependencies.
## 0.42.0 - 2023-11-02
### Changed
* bcf/reader/header: Parse header line by line.
The header parser can now build a `vcf::Header` and `StringMaps` by parsing
a raw header line by line. This makes it so that it is no longer required
to read the entire raw header into memory before parsing.
## 0.41.0 - 2023-10-26
### Changed
* bcf: Sync dependencies.
## 0.40.0 - 2023-10-23
### Added
* bcf/reader: Add builder (`bcf::reader::Builder`).
## 0.39.0 - 2023-10-19
### Changed
* bcf: Sync dependencies.
## 0.38.0 - 2023-10-12
### Changed
* bcf: Sync dependencies.
## 0.37.0 - 2023-09-21
### Changed
* bcf: Sync dependencies.
## 0.36.0 - 2023-09-14
### Removed
* bcf/lazy/record: Remove mutable reference getters.
Lazy records were not meant to be mutable. This removes
`lazy::Record::position_mut`, `lazy::Record::quality_score_mut`, and
`lazy::Record::ids_mut`.
## 0.35.0 - 2023-08-31
### Changed
* bcf: Sync dependencies.
## 0.34.0 - 2023-08-24
### Changed
* bcf: Sync dependencies.
## 0.33.0 - 2023-08-17
### Changed
* bcf: Sync dependencies.
## 0.32.0 - 2023-08-03
### Added
* bcf/indexed_reader/builder: Add index setter (`Builder::set_index`).
* bcf/indexed_reader/builder: Add `Builder::build_from_reader`.
## 0.31.0 - 2023-07-06
### Changed
* bcf: Update to indexmap 2.0.0.
### Fixed
* bcf/reader/query: Fix using parsed string maps for query ([#181]).
[#181]: https://github.com/zaeleus/noodles/issues/181
## 0.30.0 - 2023-06-29
### Added
* bcf/indexed_reader: Add builder (`indexed_reader::Builder`).
## 0.29.0 - 2023-06-15
### Added
* bcf: Add an indexed reader (`IndexedReader`).
## 0.28.0 - 2023-06-01
### Changed
* bcf: Sync dependencies.
## 0.27.0 - 2023-05-18
### Changed
* bcf: Sync dependencies.
## 0.26.0 - 2023-05-11
### Removed
* bcf/reader: Remove `Reader::read_file_format`.
`Reader::read_header` now includes checking the magic number and reading
the file format version. Calling `Reader::read_file_format` is no longer
necessary.
* bcf/writer: Remove `Writer::write_file_format`.
`Writer::write_header` now includes writing the magic number and file
format version. Calling `Writer::write_file_format` is no longer necessary.
## 0.25.0 - 2023-05-04
### Changed
* bcf: Sync dependencies.
## 0.24.0 - 2023-04-27
### Changed
* bcf: Rename `Record` to `lazy::Record`.
* bcf/async/reader: Rename `Reader::read_record` to
`Reader::read_lazy_record`.
* bcf/async/reader: Rename `Reader::records` to `Reader::lazy_records`.
* bcf/header/string_maps: Use the `IDX` field, if present, when building
string maps from a `vcf::Header`.
This now makes conversion fallible. Use `TryFrom<&vcf::Header>` instead.
* bcf/reader: Change `Reader::read_header` to return a parsed header
(`Header`).
This no longer returns a raw string. `StringMaps` are also parsed and
attached to the reader. Use `Reader::string_maps` to get a reference to the
string maps.
* bcf/reader: Change `Reader:read_record` to read a parsed record.
This now requires the header and strings map. If reading a lazy record, use
`Reader::read_lazy_record` instead.
* bcf/reader: Rename `Reader::records` to `Reader::lazy_records`.
* bcf/reader/query: Return `vcf::Record` instead of `bcf::lazy::Record`.
This now requires `Reader::query` to receive a reference to a
`vcf::Header`.
* bcf/writer: Build string maps upon writing header.
`StringMaps` are now built from the header upon calling
`Writer::write_header`. This is subsequently used as context when writing
records.
* bcf/writer: Rename `Writer::write_vcf_record` to `Writer::write_record`.
### Removed
* bcf/writer: Remove `Writer::write_record(lazy::Record)`.
Writing lazy records is not supported.
## 0.23.0 - 2023-04-06
### Changed
* bcf: Sync dependencies.
## 0.22.0 - 2023-03-14
### Added
* bcf/writer: Implement `VariantWriter` ([#150]).
[#150]: https://github.com/zaeleus/noodles/issues/150
### Fixed
* bcf/writer/vcf_record/genotypes: Fix writing dropped values ([#151]).
Trailing field values are allowed to be missing.
[#151]: https://github.com/zaeleus/noodles/issues/151
## 0.21.0 - 2023-03-03
### Added
* bcf/reader: Implement `vcf::VariantReader` ([#149]).
[#149]: https://github.com/zaeleus/noodles/pull/149
## 0.20.0 - 2023-02-03
### Changed
* bcf: Raise minimum supported Rust version (MSRV) to 1.64.0.
* bcf/record/info: Add `Info::iter` for an iterator over
`Key`-`Option<Value>` pairs.
* bcf/record/info: Change `Info::values` to return an iterator over
`Option<Value>` values.
Use `Info::iter` for fields.
* bcf/record/info: Change `Info::get` to return an `Option<Value>` value
instead of a field.
### Removed
* bcf/header: Remove `StringMap`.
This was deprecated in noodles-bcf 0.11.0. Use
`noodles_bcf::header::string_maps::StringMap` instead.
## 0.19.2 - 2022-12-02
### Fixed
* bcf/writer/vcf_writer/genotypes: Add FORMAT GT encoder for missing alleles
(i.e., `.`).
* bcf/writer/vcf_writer/genotypes: Pad integer vector for genotypes.
## 0.19.1 - 2022-11-29
### Fixed
* bcf/header/string_maps: Use file format as context when parsing records
(#137).
* bcf/writer/vcf_writer/genotypes: Add FORMAT GT encoder ([#135]).
[#135]: https://github.com/zaeleus/noodles/issues/135
[#137]: https://github.com/zaeleus/noodles/issues/137
## 0.19.0 - 2022-11-18
### Changed
* bcf: Sync dependencies.
## 0.18.0 - 2022-10-28
### Changed
* bcf: Sync dependencies.
## 0.17.0 - 2022-10-20
### Changed
* bcf: Sync dependencies.
## 0.16.0 - 2022-09-29
### Changed
* bcf: Sync dependencies.
## 0.15.0 - 2022-08-16
### Changed
* bcf: Raise minimum supported Rust version (MSRV) to 1.57.0.
### Removed
* bcf/async/reader: Remove `Builder` and `Reader::builder`.
Use `bgzf::async::reader::Builder` and construct with
`bcf::async::Reader::from` instead.
## 0.14.0 - 2022-07-05
### Changed
* bcf: Sync dependencies.
## 0.13.3 - 2022-06-08
### Fixed
* bcf: Sync dependencies.
## 0.13.2 - 2022-03-29
### Fixed
* bcf/async/reader/record: Read site from buffer ([#79]).
[#79]: https://github.com/zaeleus/noodles/issues/79
## 0.13.1 - 2022-03-02
### Fixed
* bcf: Sync dependencies.
## 0.13.0 - 2022-02-17
### Added
* bcf: Set minimum supported Rust version (MSRV) to 1.56.0 in package
manifest.
* bcf/async/reader: Add query stream.
* bcf/record: Add type alias for chromosome ID: `ChromosomeId`.
### Fixed
* bcf/writer/vcf_record/site: Avoid overflow when the alternate allele count
is `usize::MAX`.
## 0.12.0 - 2022-01-27
### Added
* bcf/async/reader: Add common methods to access the underlying reader:
`get_ref`, `get_mut`, and `into_inner`.
* bcf/reader/record/info: Handle reading INFO array values with missing raw
values.
* bcf/writer/vcf_record/site/info: Handle writing INFO array values with
missing raw values.
This allows reading/writing INFO array values that have missing raw values,
e.g., `AC=8,.`.
### Changed
* bcf/record: Change chromosome ID to a `usize`.
`CHROM` is used as an index.
* bcf/reader: Use contig string map to find contig index when querying.
The chromosome ID maps to a contig string map entry, not the header
contigs.
* bcf/writer/vcf_record/site: Ensure the record position is <= its end
position when writing `rlen`.
### Fixed
* bcf/reader/record/info: Split on delimiter when reading a character array.
* bcf/writer/record: Write filters when present.
* bcf/writer/vcf_record/site: Skip writing alternate bases when empty.
* bcf/writer/vcf_record/site: Filters with indices larger than 127 are now
valid.
* bcf/writer/vcf_record/site: Fix `rlen` calculation.
## 0.11.0 - 2022-01-13
### Added
* bcf/async/reader: Add conversion from `R` into `Reader<R>`.
### Changed
* bcf/header: Split `StringMap` from `StringMaps` (#64).
Use `bcf::header::string_maps::StringStringMap` as a replacement to what
`StringMap` was used as. It can typically be accessed using
`StringMaps::strings`.
* bcf/header/string_maps: Parsing can now fail with
`vcf::header::ParseError::StringMapPositionMismatch` if the string map
position of an entry and record-defined IDX field value do not match.
* bcf/header/string_maps: If present, the IDX field is used to determine the
position of the entry in the string map ([#64]).
* bcf/header/string_maps: Parsing (`FromStr`) and conversion
(`From<&vcf::Header>`) now builds a contig string map (also known as a
"dictionary of contigs") (#64).
It can be accessed using `StringMaps::contigs`.
* bcf/header/string_maps/string_map: The default implementation now creates
an empty map.
This used to create a default map with a `PASS` entry at position 0.
* bcf/record: `Record::try_into_vcf_record` now takes `StringMaps` instead of
`StringMap` (#64).
* bcf/record: The following now take `StringStringMap` instead of
`StringMap` (#64):
* `Filters::try_into_vcf_record_filters`
* `Info::try_into_vcf_record_info`
* `Info::get`
* `Info::values`
* `Info::try_into_vcf_record_genotypes`
* bcf/record/convert: Use contig string map to find chromosome name (#64).
* bcf/writer: `Writer::write_vcf_record` now takes `StringMaps` instead of
`StringMap`.
* bcf/writer/vcf_record: Use contig string map to find index of contig (#64).
This previously used the position of the contig in the header, but BCF
allows records to override their positions using the `IDX` field, requiring
a contig string map.
[#64]: https://github.com/zaeleus/noodles/issues/64
### Removed
* bcf/header/string_maps/string_map: Remove `Deref<Target =
IndexSet<String>>` for `StringMap`.
`StringMap` is no longer backed by an `IndexMap`.
## 0.10.0 - 2021-12-16
### Added
* bcf/reader: Add common methods to access the underlying reader: `get_ref`,
`get_mut` and `into_inner`.
* bcf/writer: Add record writer (`Writer::write_record`).
### Fixed
* bcf/writer/vcf_record/site: Fix allele count calculation.
This overcounted by 1 when there were no alternate bases.
## 0.9.0 - 2021-12-02
### Added
* bcf/record/genotypes: Add method to clear all fields (`Genotypes::clear`).
* bcf/record/info: Add methods to wrap an INFO buffer (`Info::new`), clear
all fields (`Info::clear`), retrieve a field by key (`Info::get`; [#52]),
and iterate all fields (`Info::values`).
* bcf/reader: Add conversion from `R` into `Reader<R>`.
* bcf/writer: Add conversion from `W` into `Writer<W>`.
* bcf/writer: Add common methods to access the underlying writer: `get_mut`
and `into_inner`.
[#52]: https://github.com/zaeleus/noodles/issues/52
### Changed
* bcf/header/string_map: Disable type checking when the file format is < VCF
4.3.
* bcf/reader/record/genotypes: Always use key from header.
* bcf/reader/record/site/info: Always use key from header.
* bcf/record/genotypes: Return `Genotypes` from
`Genotypes::try_into_vcf_record_genotypes`.
Use `vcf::record::Genotypes::keys` for the genotypes keys.
### Fixed
* bcf/reader/record/site/info: Allow value to be optional (#56).
[#56]: https://github.com/zaeleus/noodles/issues/56
## 0.8.0 - 2021-11-18
### Added
* bcf/record: Implement `Debug` for `Record`.
* bcf/record: Add getter for filters (`Record::filters`), IDs
(`Record::ids`), genotypes (`Record::genotypes`), info (`Record::info`),
and quality score (`Record::quality_score`).
* bcf/record: Add mutable getters for IDs (`Record::ids_mut`), position
(`Record::position_mut`) and quality score (`Record::quality_score_mut`).
### Changed
* bcf/record: `bcf::Record` is no longer backed by a contiguous buffer.
Fields are read individually when reading the record. `bcf::Record` no
longer implements `Deref<Target = [u8]>`. `Filters`, `Info`, `Genotypes`
now own their data.
## 0.7.0 - 2021-11-11
### Changed
* bcf: Update to Rust 2021.
## 0.6.1 - 2021-10-16
### Fixed
* bcf: Sync dependencies.
## 0.6.0 - 2021-10-01
### Added
* bcf: Increase visibility of `reader` module ([#37]).
This allows public access to the reader iterators `Records` and `Query`.
[#37]: https://github.com/zaeleus/noodles/pull/37
## 0.5.2 - 2021-09-19
### Fixed
* bcf: Sync dependencies.
## 0.5.1 - 2021-09-01
### Fixed
* bcf: Sync dependencies.
## 0.5.0 - 2021-08-19
### Changed
* bcf: Update to tokio 1.10.0.
* bcf/async: I/O builders are now owned/consuming builders.
This fixes the terminal method not being able to move out of a mutable
reference.
### Fixed
* bcf: Define features to enable for Docs.rs.
## 0.4.0 - 2021-08-11
### Added
* bcf/async: Add async reader (`bcf::AsyncReader`).
This can be enabled with the `async` feature.
## 0.3.1 - 2021-08-04
### Fixed
* bcf: Sync dependencies.
## 0.3.0 - 2021-07-30
### Added
* bcf/header/string_map: Implement conversion from `vcf::Header`.
## 0.2.0 - 2021-07-21
### Added
* bcf/reader: Accept any `BinningIndex` to query.
### Fixed
* bcf: Fixed documentation link in package manifest ([#31]).
[#31]: https://github.com/zaeleus/noodles/issues/31
## 0.1.0 - 2021-07-14
* bcf: Initial release.