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sam/changelog: Update changelog
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zaeleus committed Jan 25, 2024
1 parent 99918fd commit 0820faa
Showing 1 changed file with 13 additions and 18 deletions.
31 changes: 13 additions & 18 deletions noodles-sam/CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,18 +8,17 @@
record.

The alignment record buffer is renamed to `RecordBuf`. This also introduces
traits for all fields.
traits for field buffers.

* sam/async/io/reader: Add record reader (`Reader::read_record`).

* sam/io/reader: Add records iterator (`Reader::records`).

* sam/record: Add wrappers for read name (`record::ReadName`) and template
length (`record::TemplateLength`).
* sam/record: Add wrapper for name (`record::Name`).

* sam/record: Add method to get reference sequence ID
(`Record::reference_sequence_id`) and mate reference sequence ID
(`Record::mate_reference_sequence_id`). .
(`Record::mate_reference_sequence_id`).

* sam/record/data/field/value/array: Add values wrapper (`Values`).

Expand All @@ -39,10 +38,6 @@
* sam/alignment/io/write: Change `Write::write_record` to accept `&dyn
crate::alignment::Record`.

* sam/alignment/iter/pileup: Work with `Record` objects.

Instantiating `Pileup` now requires a `Header`.

* sam/alignment/record_buf: Change name to raw buffer (`record_buf::Name`).

* sam/alignment/record_buf: Change sequence to raw bases
Expand All @@ -52,12 +47,12 @@
(`record_buf::QualityScores`).

* sam/header: Change `ReferenceSequences`, `ReadGroup`, and `Program` keys to
byte strings (`Vec<u8>`).
byte strings (`BString`).

* sam/header: Change `Comments` to a list of byte strings (`Vec<Vec<u8>>`).
* sam/header: Change `Comments` to a list of byte strings (`Vec<BString>`).

* sam/header/record/value/map: Change `OtherFields` values to byte strings
(`Vec<u8>`).
(`BString`).

* sam/io/reader: Rename record to record buf and lazy record to record.

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* `Records` => `RecordBufs`, and
* `Reader::read_lazy_record` => `Reader::read_record`.

* sam/io/reader: Return an iterator over sam::Record from queries
* sam/io/reader: Return an iterator over `sam::Record` from queries
(`Reader::query` and `Reader::query_unmapped`).

`Reader::query_unmapped` no longer needs a reference to the header.
Expand All @@ -77,15 +72,15 @@

This also changes `Record::read_name` to `Record::name`.

* sam/record/cigar: Move `Cigar` to `alignment::record_buf::Cigar`.
* sam/record: Move scalar values to `alignment::record` module.

`op` is moved to `alignment::record::cigar::op`.
Replace usages of, e.g., `sam::record::Flag` with
`sam::alignment::record::Flag`.

* sam/record/data/field: Replace `Value` with
`crate::alignment::record::data::field::Value`.
* sam/record: Move buffers to `alignment::record_buf` module.

* sam/record/data/field/value: Replace `Array` with
`crate::alignment::record::data::field::value::Array`.
Replace usages of, e.g., `sam::record::Cigar` with
`sam::alignment::record_buf::Cigar`.

### Removed

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