# Changelog
## 0.19.0 - 2022-09-29
### Added
* vcf/header/record/value/map/tag: Implement `AsRef<str>` for `Tag`.
## 0.18.0 - 2022-08-16
### Added
* vcf/header/record/value/map: Add builder (`Builder<I>`).
* vcf/header/record/value/map/contig: Add mutable getter for length
(`Contig::length_mut`) ([#99]).
* vcf/header/contig/value/map/contig: Add name wrapper (`Name`).
[#99]: https://github.com/zaeleus/noodles/issues/99
### Changed
* vcf: Raise minimum supported Rust version (MSRV) to 1.57.0.
* vcf/header: VCF header records parsed from structured lines are now map
values (`noodles_vcf::header::record::value::Map`).
This moves record types (`AlternativeAllele`, `Contig`, `Filter`, `Format`,
`Info`, and `Meta`) to map values `Map<I>`, where `I` is a specialized map
type. A map is required to have an `ID` field; an inner `I` type that can
have required standard fields; and can include optional fields, where the
key is a nonstandard tag (`tag::Other`).
* vcf/header: Change the key of `Contigs` to `contig::Name`.
* vcf/header/record: Record holds a parsed record variant instead a key-value
pair.
* vcf/header/record/key: Split standard (`Standard`) and nonstandard
(`Other`) keys.
* vcf/header/record/value/map: Structured lines can no longer have duplicate
field tags.
* vcf/header/contig/value/map/contig: Change length to `usize`.
* vcf/header/record/value/map/contig: Rename `Contig::len` to
`Contig::length`.
### Deprecated
* vcf/header: Deprecate `Header::records`, `Header::records_mut`,
`header::Records`.
Use `Header::other_records`, `Header::other_records_mut`,
`header::OtherRecords`, respectively, instead.
### Fixed
* vcf/header/record/value: Write surrounding angle brackets for structs.
### Removed
* vcf/header: Remove `Pedigree`, and `Sample`.
Use `Map<Other>` instead.
## 0.17.0 - 2022-07-05
### Changed
* vcf: Sync dependencies.
## 0.16.1 - 2022-06-09
### Fixed
* vcf: Sync dependencies.
## 0.16.0 - 2022-06-08
### Changed
* vcf/record/position: Change underlying type to `usize`.
### Removed
* vcf/record/position: Remove conversion to `i32` (`From<Position> for i32`).
Use conversion to `usize` (`From<Position> for usize`) instead.
* vcf/record/position: Remove fallible conversion from `i32` (`TryFrom<i32>
for Position`).
Use conversion from `usize` instead (`From<usize> for Position`).
* vcf/record/position: Remove `TryFromIntError`.
This is no longer used.
## 0.15.0 - 2022-03-29
### Changed
* vcf: Move INFO and FORMAT keys from record field to header record.
* vcf/record/genotypes: Add `parse` method.
This uses FORMAT header records for type information.
* vcf/record/genotypes/genotype: Rename `from_str_keys` to `parse`.
`Genotype` now uses FORMAT header records for type information.
* vcf/record/genotypes/genotype/field: Rename `from_str_key` to
`from_str_format`.
`Field` now uses FORMAT header records for type information.
* vcf/record/genotypes/genotype/field/value: Rename `from_str_key` to
`from_str_format`.
`Value` now uses FORMAT header records for type information.
* vcf/record/info/field/value: Rename `from_str_key` to `from_str_info`.
`Value` now uses INFO header records for type information.
* vcf/record/parser: Use VCF header when parsing genotypes.
### Removed
* vcf/header: Remove record field keys.
* vcf/record/genotypes/genotype: Remove deprecated `from_str_format`.
Use `Genotype::parse` instead.
## 0.14.1 - 2022-03-02
### Fixed
* vcf: Sync dependencies.
## 0.14.0 - 2022-02-17
### Added
* vcf: Set minimum supported Rust version (MSRV) to 1.56.0 in package
manifest.
## 0.13.0 - 2022-01-27
### Added
* vcf/record/info: Add `clear` method to remove all fields from the info
map.
* vcf/record/position: Implement `Display`.
### Changed
* vcf/record/info/field/value: Allow missing values in arrays.
Array values (`Value::IntegerArray`, `Value::FloatArray`,
`Value::CharacterArray`, and `Value::StringArray`) now wrap a vector of
optional values, rather than values, e.g., `Vec<Option<i32>>` rather than
`Vec<i32>`.
### Deprecated
* vcf/record/genotypes/genotype: Deprecate `Genotype::from_str_format`.
Use `Genotype::from_str_keys` instead.
### Fixed
* vcf/record: Handle missing INFO END field value as no field.
When a record has an INFO END field with a missing a value, i.e., `END=.`,
it is treated as missing rather than invalid.
## 0.12.0 - 2022-01-13
### Added
* vcf/header: Add mutable getters for `vcf::Header` fields ([#65]).
* vcf/header: Add immutable and mutable getters for unstructured
`vcf::Header` fields ([#69]).
* vcf/header: Add `Records` type alias for records (`IndexMap<String,
Vec<Record>`).
* vcf/header/parser: Add `ParseError::StringMapPositionMismatch(actual,
expected)`.
This is returned when the IDX field value of a record does not match its
relative position in a string map. It is primarily used in BCF.
* vcf/record: Add mutable getters for genotypes, reference bases, and
alternate bases ([#67]).
* vcf/record/alternate_bases: Implement `DerefMut` ([#67]).
* vcf/record/genotypes: Add mutable getter for keys ([#67]).
* vcf/record/genotypes: Add method to return whether there are any samples
(`Genotypes::is_empty`).
* vcf/record/genotypes/genotype: Implement `DerefMut` ([#67]).
* vcf/record/genotypes/keys: Implement `DerefMut` ([#67]).
* vcf/record/position: Derive `PartialOrd` and `Ord` ([#70]).
* vcf/record/quality_score: Derive `PartialOrd` ([#70]).
* vcf/record/reference_bases: Implement `DerefMut` ([#67]).
[#65]: https://github.com/zaeleus/noodles/issues/65
[#67]: https://github.com/zaeleus/noodles/pull/67
[#69]: https://github.com/zaeleus/noodles/pull/69
[#70]: https://github.com/zaeleus/noodles/pull/70
### Changed
* vcf/header/contig: Parse `IDX` field from a raw record ([#64]).
This was previously added to the other fields map but is now a field on
`Contig`.
### Fixed
* vcf/header/contig: Write the IDX field value as an integer rather than a
string ([#64]).
[#64]: https://github.com/zaeleus/noodles/issues/64
## 0.11.1 - 2021-12-09
### Fixed
* vcf: Sync dependencies.
## 0.11.0 - 2021-12-02
### Added
* vcf/header/format: Add conversion from `vcf::header::Record` to
`vcf::header::Format` with a file format constraint.
* vcf/header/info: Add conversion from `vcf::header::Record` to
`vcf::header::Info` with a file format constraint.
* vcf/record/genotypes: Add parser.
* vcf/record/genotypes/keys: Implement `Default`.
### Changed
* vcf/async/reader: `Reader::{records, query}` now parse records with the
header.
* vcf/reader: `Reader::{records, query}` now parse records with the header.
* vcf/record: Move `Format` under genotypes module as `Keys`.
* vcf/record/genotypes: Print keys on display.
* vcf/record/genotypes/keys: Prefer key from header.
* vcf/record/genotypes/keys: Allow empty genotypes keys.
* vcf/record/info/field: Prefer key from header.
* vcf/record/info/field: Allow value to be optional.
### Deprecated
* vcf/record: Deprecate `vcf::record::Format`.
Use `vcf::record::genotypes::Keys` instead.
### Removed
* vcf/record/builder: Remove `Builder::{add_genotype,set_format}`.
Use `Builder::set_genotypes` instead.
* vcf/record: Remove `ParseError::{InvalidFormat,InvalidGenotype}`.
These are now wrapped by `ParseError::InvalidGenotypes`.
* vcf/record/genotypes/keys: Remove `TryFromKeyVectorError::Empty`.
Empty genotype keys are now allowed.
* vcf/record/genotypes: Remove `From<Vec<Genotype>>`.
Use `Genotypes::new` instead.
## 0.10.0 - 2021-11-18
### Added
* vcf/reader: Add common methods to access the underlying reader: `get_ref`,
`get_mut`, and `into_inner`.
* vcf/record/genotypes/genotype/field: Add mutable getter for value
(`Field::value_mut`).
### Changed
* vcf/header/format: Disable type checking when the file format is < VCF 4.3
(#41).
* vcf/header/info: Disable type checking when the file format is < VCF 4.3
(#41).
[#41]: https://github.com/zaeleus/noodles/issues/41
## 0.9.0 - 2021-11-11
### Added
* vcf/record: Add mutable getters for chromosome (`Record::chromosome_mut`),
filters (`Record::filters_mut`), IDs (`Record::ids_mut`), info
(`Record::info_mut`; [#52]), position (`Record::position_mut`), and quality
score (`Record::quality_score_mut`).
* vcf/record/ids: Add ID wrapper.
* vcf/record/info/field: Add mutable getter for value (`Field::value_mut`;
[#52]).
* vcf/writer: Add common methods to access the underlying writer: `get_mut`
and `into_inner`.
[#52]: https://github.com/zaeleus/noodles/issues/52
### Changed
* vcf: Update to Rust 2021.
* vcf/header/record/parser: Remove alphanumeric constraint on field keys.
* vcf/record/info: `Info` no longer implements `Deref`.
Use `AsRef<IndexMap<field::Key, Field>>` to access the lower level ordered
map.
* vcf/record/quality_score: Wrap only non-missing values.
The missing quality score state is moved to `vcf::Record` as an `Option`.
### Removed
* vcf/record/filters: Remove missing variant.
`Filters::Missing` is removed in favor of using an `Option` in
`vcf::Record`.
## 0.8.0 - 2021-10-16
### Added
* vcf/record: Wrap `Genotype` field (`vcf::record::Genotypes`) ([#42]).
This creates a new type for `Vec<vcf::record::genotypes::Genotype>`.
* vcf/record/genotypes: Add convenience method to return a list of parsed
genotype (`GT`) fields (`Genotypes::genotypes`) ([#42]).
* vcf/record/genotypes/genotype: Add convenience method to parse the genotype
(`GT`) field (`Genotype::genotype`) ([#42]).
* vcf/record/genotypes/genotype/field/value/genotype: Add conversion from
`Vec<Allele>` to `Genotype` ([#43]).
* vcf/record/genotypes/genotype/field/value/genotype/allele: Add accessors
for `position` and `phasing` ([#43]).
[#42]: https://github.com/zaeleus/noodles/issues/42
[#43]: https://github.com/zaeleus/noodles/pull/43
### Changed
* vcf/record: Move `genotype` under `genotypes` module.
### Deprecated
* vcf/record: Deprecated `genotype` and `Genotype` public exports.
Use `noodles_vcf::record::genotypes::{genotype, Genotype}` instead.
## 0.7.0 - 2021-10-01
### Added
* vcf: 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
## 0.6.2 - 2021-09-23
### Fixed
* vcf: Sync dependencies.
## 0.6.1 - 2021-09-19
### Fixed
* vcf: Sync dependencies.
## 0.6.0 - 2021-09-01
### Changed
* vcf: Update to nom 7.0.0.
## 0.5.0 - 2021-08-19
### Changed
* vcf: Update to tokio 1.10.0.
### Fixed
* vcf: Define features to enable for Docs.rs.
## 0.4.0 - 2021-08-11
### Added
* vcf/async: Add async reader (`vcf::AsyncReader`).
* vcf/async: Add async writer (`vcf::AsyncWriter`).
Async I/O can be enabled with the `async` feature.
## 0.3.0 - 2021-08-04
### Added
* vcf/header/alternative_allele: Accept `Into<String>` for description in
constructor.
## 0.2.0 - 2021-07-30
### Added
* vcf/header/contig: Accept `Into<String>` arguments in constructor.
* vcf/header/filter: Accept `Into<String>` arguments in constructor.
## 0.1.1 - 2021-07-21
### Fixed
* vcf: Fixed documentation link in package manifest ([#31]).
[#31]: https://github.com/zaeleus/noodles/issues/31
## 0.1.0 - 2021-07-14
* vcf: Initial release.