# Changelog
## 0.21.0 - 2022-10-28
### Added
* cram/async: Add async writer (`cram::AsyncWriter`).
### Fixed
* cram/reader/header_container: Truncate data by header length.
This is required if the header text is padded rather than using a new block
for padding.
## 0.20.0 - 2022-10-20
### Added
* cram: Add CRAM 3.1 write support ([#107]).
The format of CRAM 3.1 is structurally the same as 3.0, but 3.1 includes
additional block content compression methods: rANS Nx16, adaptive
arithmetic coder, fqzcomp, and name tokenizer.
* cram/codecs: Add fqzcomp encoder.
* cram/codecs: Increase visibilities of `aac::Flags`, `rans_4x8::Order`, and
`rans_nx16::Flags`.
* cram/codecs/name_tokenizer/encode: Add `DIGITS0`, `DIGITS`, `DELTA`,
`DELTA0`, and `MATCH` tokens.
### Changed
* cram: Raise minimum supported Rust version (MSRV) to 1.62.0.
* cram/writer: Calculate and write missing MD5 checksums (`M5`) in the
reference sequence dictionary.
### Fixed
* cram/codecs/aac/encode: Fix serialization of the max symbol for order-0 and
1 encoders.
* cram/codecs/aac/encode: Disable bit packing if the input has more than 16
symbols.
* cram/codecs/fqzcomp/decode: Fix reading records with varying lengths.
* cram/codecs/name_tokenizer/decode: Add missing mutable `DUP` reader.
* cram/codecs/name_tokenizer/decode: Fix setting `TYPE` reader when reading
token byte streams.
* cram/codecs/name_tokenizer/encode: Strip final separator before splitting
names.
* cram/codecs/rans_4x8/encode: Fix run-length calculation when writing
frequencies.
* cram/codecs/rans_4x8/encode: Avoid scaling frequencies to 0 during
normalization.
* cram/codecs/rans_4x8/encode: Ensure the sum of the normalized frequencies
equals the scaling factor.
* cram/codecs/rans_4x8/encode/order_1: Fix order of rANS state
renormalizations.
* cram/codecs/rans_nx16/encode: Fix run-length calculation when writing
frequencies.
* cram/codecs/rans_nx16/encode: Avoid scaling frequencies to 0 during
normalization.
* cram/codecs/rans_nx16/encode: Handle 0 RLE symbols.
* cram/codecs/rans_nx16/encode: Disable rANS encoding when the input is too
small.
* cram/codecs/rans_nx16/encode: Disable bit packing if the input has more
than 16 symbols.
* cram/codecs/rans_nx16/encode: Ensure the sum of the normalized frequencies
equals the scaling factor.
* cram/codecs/rans_nx16/encode/order_1: Fix order of rANS state
renormalizations.
[#107]: https://github.com/zaeleus/noodles/issues/107
## 0.19.0 - 2022-09-29
### Added
* cram/codecs: Add rANS Nx16, adaptive arithmetic coder, and name tokenizer
encoders.
* cram/data_container: Add block content-encoder map
(`BlockContentEncoderMap`) to assign encoders to block contents (core, data
series, and tag values).
* cram/writer/builder: Add setter for block content-encoder map.
### Changed
* cram: Increased visibilities of `cram::writer`,
`data_series_encoding_map::DataSeries`, and `tag_ids_dictionary::Key`.
* cram/writer/builder: Change `build` to `build_with_writer`.
`writer::Builder` no longer holds the inner reader.
### Fixed
* cram/container/block: Add terminators (`NUL`) to decoded names.
### Removed
* cram/writer: Remove `Writer::builder`.
Use `cram::writer::Builder` directly instead.
## 0.18.0 - 2022-08-16
### Changed
* cram: Raise minimum supported Rust version (MSRV) to 1.59.0.
## 0.17.0 - 2022-07-05
### Changed
* cram: Sync dependencies.
## 0.16.0 - 2022-06-08
### Added
* cram/async/reader: Add records stream (`AsyncReader::records`).
### Changed
* cram/async/reader/container/header: Verify the expected CRC32 checksum of
the container header.
* cram/data_container/slice: Template size for records with downstream mates
is now calculated from the leftmost to rightmost base, regardless of
orientation.
* cram/data_container/slice: Verify reference sequence checksum.
§ 11 "Reference sequences" (2021-11-15): "All CRAM reader implementations
are expected to check for reference MD5 checksums and report any missing or
mismatching entries."
* cram/data_container/slice/builder: Match mate by read name.
* cram/reader/container/block: Verify the expected CRC32 checksum of the
block.
* cram/reader/container/header: Verify the expected CRC32 checksum of the
container header.
* cram/record/convert: Change `Record::try_into_sam_record` to
`Record::try_into_alignment_record`.
This now takes a `&sam::alignment::Record`.
### Fixed
* cram/data_container/builder: Disable encoding alignment start positions as
deltas when the container has multi-reference slices.
* cram/data_container/slice: Resolve read group ID.
This adds the `RG` field with the corresponding read group ID to data.
* cram/data_container/slice: Resolve read name if none is set.
### Deprecated
* cram/record/resolve: Deprecate `resolve_features`.
Use `Features::try_into_cigar` instead.
### Removed
* cram/record: Remove `sam::AlignmentRecord`.
Convert to an alignment record (`Record::try_into_alignment_record`)
instead.
## 0.15.0 - 2022-04-14
### Added
* cram/reader: Add query iterator (`Reader::query`).
* cram/reader/data_container/compression_header/encoding: Add Golomb and
Golomb-Rice encoding decoders.
* cram/writer/data_container/compression_header/encoding: Add Golomb and
Golomb-Rice encoding writers.
These see no usage in practice, but they are still in the spec (§ 13.8 and
§ 13.9, respectively). They are only added for completeness.
### Changed
* cram/data_container/slice/builder: Slices can now be multi-reference.
### Fixed
* cram/container: Return error (`TryFromSamHeaderError::InvalidHeaderLength`)
when header length is too large.
## 0.14.0 - 2022-03-29
### Added
* cram/reader: Implement `sam::AlignmentReader`.
* cram/record: Add conversion from an alignment record to a CRAM record.
* cram/record/features: Add conversion from SAM CIGAR operations.
* cram/writer: Implement `sam::AlignmentWriter`.
### Changed
* cram/crai/record: Change reference sequence ID to an `Option<usize>`;
alignment start, `Option<Position>`; and alignment span, `usize`.
* cram/record: Move `mapping_quality`, `read_name`, and `quality_scores` to
the implementation of `sam::AlignmentRecord`.
* cram/record: Rename `flags` to `cram_flags`.
* cram/record: Wrap read name as `sam::record::ReadName`.
* cram/record: Wrap quality scores as `sam::record::QualityScores`.
* cram/record: Wrap sequence as `sam::record::Sequence`.
* cram/record: Change tags to `sam::record::Data`.
* cram/record: Change alignment start and next mate alignment start to a
`Position`.
* cram/record: Change distance to next fragment to an `Option<usize>`.
This distance can only be forward (_CRAM format specification (version
3.0)_ (2021-10-15) § 8.4 "Compression header block": "... NF can only refer
to a record later within [the] slice.") and is only set when the "has mate
downstream" flag is set.
* cram/record: Change read group ID to an `Option<usize>`.
* cram/record: Change reference sequence ID and next fragment reference
sequence ID to an `Option<usize>`.
* cram/record/convert: Accept `sam::Header` instead of `ReferenceSequences`.
* cram/record/feature: Change underlying data types:
* bases as `sam::record::sequence::Base`,
* lengths as `usize`,
* positions as `Position`,
* quality scores as `sam::record::quality_scores::Score`, and
* substitution as `substitution::Value`.
* cram/record/resolve: Merge adjacent CIGAR operations.
For example, instead of 1M1M2M, this is now 4M.
* cram/record/tag/key: Change tag to a `sam::record::data::field::Tag`.
* cram/writer: Make a reference sequence repository optional.
Use `Builder::set_reference_sequence_repository` to set one.
* cram/writer: A writer no longer has to be constructed with a header.
However, `Writer::write_record` and `Writer::try_finish` must be called
with a reference to a `sam::Header` now.
### Fixed
* cram/data_container/slice: Only attempt to resolve quality scores for
mapped records.
* cram/data_container/slice/builder: Detach all records before writing.
The slice builder does not yet calculate mate distances, so all records are
currently written as detached.
* cram/data_container/slice/builder: Normalize sequence for MD5 digest
calculation.
* cram/reader/data_container: Disallow unexpected block content types when
reading a data container.
* cram/record/convert: Create read group (`RG`) data field if a read group ID
is set.
* cram/record/convert: Only convert CIGAR to features for mapped records.
Unmapped records cannot have features.
* cram/record/resolve: Handle `Scores` feature when resolving quality scores.
* cram/writer: Avoid possible wrapping when casting `usize` to `i32`.
### Removed
* cram/record: Remove `ReadGroupId`.
Use `usize` instead.
* cram/record: Remove `Tag`.
Use `sam::record::data::Field` instead.
* cram/writer: Remove `Drop`.
A call to `Writer::try_finish` must be made before the writer is dropped.
## 0.13.0 - 2022-03-02
### Added
* cram/data_container/slice: Add slice records resolver.
This resolves mates, read names, bases, and quality scores.
* cram/record: Add features wrapper (`Features`).
* cram/record: Implement `sam::RecordExt`.
* cram/record/feature/code: Implement `TryFrom<u8>`.
* cram/record/feature/code: Add conversion to `u8`.
* cram/record/resolve: Add quality scores resolver.
* cram/record/resolve: Allow base resolution when there is no reference
sequence available.
Even when both an external reference sequence and embedded reference
sequence are missing, it is still possible to resolve bases.
* cram/writer: Add builder.
* cram/writer/builder: Add options to change applicable preservation map
values, i.e., whether to preserve read names and whether to encode record
alignment start positions as deltas.
### Changed
* cram/data_container/builder: Decrease max slice count to 1.
* cram/data_container/slice/builder: Increase max record count to 10240.
* cram/reader: `records` uses a `fasta::Repository` instead of
`&[fasta::Record]`.
This avoids having to do an initial read of all reference sequences. It
also now requires the SAM header.
* cram/reader/records: Resolve bases and quality scores when reading records.
This previously only resolved mates and read names.
* cram/record/convert: `Record::try_into_sam_record` now assumes the record
is fully resolved before conversion.
* cram/record/read_group_id: Change underlying type to a `usize`.
Use `From<usize>` instead of `From<i32>`.
* cram/record/resolve: `resolve_bases` takes a `sam::record::Position`
instead of an `i32` for `alignment_start`.
* cram/writer: Use reference sequence repository (`fasta::Repository`) and
SAM header (`sam::Header`) when writing records.
### Deprecated
* cram/record/feature/code: Deprecate fallible conversion from `char`.
This also deprecates `TryFromCharError`. Use `TryFrom<u8>` instead.
* cram/record/feature/code: Deprecate conversion to `char`.
Convert to a `u8` instead.
### Fixed
* cram/container: Only set alignment start and span when the container has
single-reference slices of the same reference.
* cram/container: Ensure all slices in the container have the same reference
sequence ID.
* cram/data_container/slice/builder: Update substitution codes before writing
records.
* cram/data_container/slice/builder: Only set alignment start and span when
the slice is a single-reference slice.
* cram/data_container/compression_header/preservation_map/substitution_matrix/builder:
Read read base from read bases.
* cram/record/convert: Only resolve features when the record is mapped.
* cram/writer/record: Fix data series type when the features code encoding is
missing.
### Removed
* cram/data_container/slice: Remove `resolve_mates`.
Use `Slice::resolve_records` instead.
* cram/record/read_group_id: Remove conversion to and from `i32`.
Convert from `usize` instead.
* cram/record/resolve: Remove `resolve_bases`.
Base resolution can only be guaranteed when the slice is available, as it
may contain an embedded reference sequence.
Use `Slice::resolve_records` instead.
## 0.12.0 - 2022-02-17
### Added
* cram: Set minimum supported Rust version (MSRV) to 1.56.0 in package
manifest.
* cram/container/block/compression_method: Add decoder support for CRAM 3.1
(draft) block compression methods: rANS Nx16, adaptive arithmetic coder,
fqzcomp, and name tokenizer.
* cram/record/resolve: Add read base (`B`) base resolver.
### Changed
* cram: Write 0 for alignment start and alignment span for slices with
unmapped records when indexing.
* cram/data_container/slice: The mate resolver (`Slice::resolve_mates`) is
now fallible.
* cram/record: `Record::alignment_end` now returns
`Option<io::Result<sam::record::Position>>`.
### Fixed
* cram/data_container/slice: Fix template size calculation when resolving
mates.
* cram/writer/data_container/compression_header/data_series_encoding_map:
Avoid truncating data length.
## 0.11.0 - 2022-01-27
### Added
* cram/record/resolve: Add bases (`b`) base resolver.
### Fixed
* cram/async/reader/record: Read feature code as byte.
* cram/huffman: Fix read length from bit reader.
* cram/reader/record: Read feature code as byte.
This was incorrectly being read as an ITF-8 value.
## 0.10.0 - 2022-01-13
### Added
* cram/record: Mapping quality is now stored as an `Option`.
Valid mapping qualities are between 0 and 254, inclusive (`Some`). A
mapping quality of 255 is considered to be missing (`None`).
## 0.9.0 - 2021-12-16
### Changed
* cram: Update to [md-5 0.10.0].
[md-5 0.10.0]: https://crates.io/crates/md-5/0.10.0
## 0.8.3 - 2021-12-09
### Fixed
* cram: Sync dependencies.
## 0.8.2 - 2021-12-02
### Fixed
* cram: Require tokio's `fs` feature as a dependency ([#62]).
[#62]: https://github.com/zaeleus/noodles/issues/62
## 0.8.1 - 2021-11-18
### Fixed
* cram: Sync dependencies.
## 0.8.0 - 2021-11-11
### Added
* cram/crai: Add convenience write function (`crai::write`).
* cram/crai/async: Add async writer (`crai::AsyncWriter`).
* cram/crai/async: Add convenience write function (`crai::r#async::write`).
### Changed
* cram: Update to Rust 2021.
## 0.7.0 - 2021-10-16
### Added
* cram/data_container/compression_header/data_series_encoding_map/
data_series: Add legacy TC and TN data series.
These are no longer used in CRAM 3.0 but still need to be handled. See
samtools/hts-specs@9a0513783826516fb8086ecf82d13631a2292f75.
* cram/record/resolve: Handle reference skip feature in sequence resolver.
## 0.6.1 - 2021-10-02
### Fixed
* cram: Sync dependencies.
## 0.6.0 - 2021-10-01
### Added
* cram/reader: Add common methods to access the underlying reader: `get_ref`,
`get_mut`, and `into_inner`.
### Fixed
* cram/rans/decode/order_1: Fix overflow when reading frequencies.
## 0.5.1 - 2021-09-23
### Fixed
* cram/async/reader/container/header: Fix reading starting position on the
reference.
* cram/async/reader/data_container/slice/header: Fix reading alignment start.
## 0.5.0 - 2021-09-19
### Added
* cram/crai/record: Implement `Display`.
* cram/reader: Add data container reader.
This can be used to manually read records from slices.
* cram/record: Add conversion to SAM record
(`cram::Record::try_into_sam_record`).
### Changed
* cram/record: Change alignment start to a `sam::record::Position`.
* cram/record: Change next mate alignment start to a `sam::record::Position`.
* cram/record/resolve: Pass compression header rather than substitution
matrix.
The compression header includes the substitution matrix in the preservation
map.
### Fixed
* cram/async/reader/data_container/slice/header: Read remainder of stream as
optional tags.
* cram/reader/container: Avoid casts that may truncate.
* cram/reader/data_container/compression_header/encoding: Avoid casts that
may truncate.
Buffer sizes that convert from `Itf8` to `usize` now check whether they are
in range.
* cram/reader/data_container/slice/header: Read remainder of stream as
optional tags.
* cram/record/resolve: Increment feature position with operations that
consume the read.
* cram/record/resolve: Include last feature position.
## 0.4.0 - 2021-09-01
### Added
* cram/async/reader: Add data container reader.
* cram/reader: Add data container reader.
This can be used to manually read records from slices.
### Changed
* cram/record: `Record::read_length` is now stored as a `usize`.
### Fixed
* cram/reader/data_container/compression_header: Avoid casts that may
truncate.
Buffer sizes that convert from `Itf8` to `usize` now check whether they are
in range.
## 0.3.0 - 2021-08-19
### Added
* cram/async: Add async header reader (`cram::AsyncReader`).
This is a partial async CRAM reader that can only read the file definition
and file header.
* cram/crai/async: Add async reader (`crai::AsyncReader`).
* cram/crai/async: Add async writer (`crai::AsyncWriter`).
Async I/O can be enabled with the `async` feature.
## 0.2.2 - 2021-08-11
### Fixed
* cram: Sync dependencies.
## 0.2.1 - 2021-07-30
### Fixed
* cram: Sync dependencies.
## 0.2.0 - 2021-07-21
### Added
* cram/record/tag: Add conversion from `Tag` to `sam::record::data::Field`.
### Fixed
* cram: Fixed documentation link in package manifest ([#31]).
[#31]: https://github.com/zaeleus/noodles/issues/31
## 0.1.0 - 2021-07-14
* cram: Initial release.