From 0820faa60ebe9d56b5d10f5e95f9763fbb67ca87 Mon Sep 17 00:00:00 2001 From: Michael Macias Date: Thu, 25 Jan 2024 10:04:56 -0600 Subject: [PATCH] sam/changelog: Update changelog --- noodles-sam/CHANGELOG.md | 31 +++++++++++++------------------ 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/noodles-sam/CHANGELOG.md b/noodles-sam/CHANGELOG.md index 6c0c65a49..6b7cdc98b 100644 --- a/noodles-sam/CHANGELOG.md +++ b/noodles-sam/CHANGELOG.md @@ -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`). @@ -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 @@ -52,12 +47,12 @@ (`record_buf::QualityScores`). * sam/header: Change `ReferenceSequences`, `ReadGroup`, and `Program` keys to - byte strings (`Vec`). + byte strings (`BString`). - * sam/header: Change `Comments` to a list of byte strings (`Vec>`). + * sam/header: Change `Comments` to a list of byte strings (`Vec`). * sam/header/record/value/map: Change `OtherFields` values to byte strings - (`Vec`). + (`BString`). * sam/io/reader: Rename record to record buf and lazy record to record. @@ -68,7 +63,7 @@ * `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. @@ -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