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fix: update noodles group #447

Merged
merged 2 commits into from
May 8, 2024
Merged

fix: update noodles group #447

merged 2 commits into from
May 8, 2024

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tedil
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@tedil tedil commented May 7, 2024

Update noodles group to current versions. Quite a lot of the API changed since the last time the noodles group was updated for annonars, but in short:

  • most Key structs have been replaced by Strings,
  • record.chromosome() is now record.reference_sequence_name() and is also a String (or rather &str),
  • record.position() is now record.variant_start() (and is an optional position now, because apparently for telomeric breakends there is no variant_start),
  • lazy::Record is now the default Record while the old Record is now RecordBuf; there's also a Record trait, which is currently unused.
  • IndexedReaders now use bgzf::io::Seek constraints etc
  • a lot of custom structs now simply wrap IndexSet<String> or similar (e.g. Filters)

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codecov bot commented May 7, 2024

Codecov Report

Attention: Patch coverage is 76.30058% with 41 lines in your changes are missing coverage. Please review.

Project coverage is 73.92%. Comparing base (41512ca) to head (9104395).

Files Patch % Lines
src/freqs/cli/import/mod.rs 0.00% 7 Missing ⚠️
src/freqs/cli/import/auto.rs 0.00% 5 Missing ⚠️
src/freqs/cli/import/mt.rs 0.00% 5 Missing ⚠️
src/freqs/cli/import/xy.rs 0.00% 5 Missing ⚠️
src/gnomad_sv/cli/import/gnomad_cnv4.rs 0.00% 5 Missing ⚠️
src/helixmtdb/pbs.rs 75.00% 5 Missing ⚠️
src/freqs/cli/import/reading.rs 83.33% 3 Missing ⚠️
src/common/noodles.rs 92.85% 1 Missing ⚠️
src/freqs/serialized/auto.rs 0.00% 1 Missing ⚠️
src/freqs/serialized/mt.rs 0.00% 1 Missing ⚠️
... and 3 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #447      +/-   ##
==========================================
- Coverage   73.93%   73.92%   -0.01%     
==========================================
  Files          79       79              
  Lines        8307     8308       +1     
==========================================
  Hits         6142     6142              
- Misses       2165     2166       +1     

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@tedil tedil changed the title enhancement: update noodles group fix: update noodles group May 8, 2024
@tedil tedil requested a review from holtgrewe May 8, 2024 08:39
@tedil tedil merged commit 683c84d into main May 8, 2024
9 of 10 checks passed
@tedil tedil deleted the update-noodles branch May 8, 2024 09:22
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2 participants