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collapse annotation helper types #406

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merged 10 commits into from
Apr 17, 2024
Merged

collapse annotation helper types #406

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0ea91a1
Collapse PerfectMatch and SemiPerfectMatch into Alignment.
macklin-10x Mar 21, 2024
a1a19bc
Move Offset type into sole function that uses it.
macklin-10x Mar 21, 2024
74e9348
Provide an explicit implementation of sort by ref_id.
macklin-10x Mar 21, 2024
b56cee5
Fore PreAnnotation to specify a cmp strategy.
macklin-10x Mar 21, 2024
e675347
Re-express initial alignment type in terms of ref_start and create an…
macklin-10x Mar 21, 2024
8b00619
Collapse the two alignment types.
macklin-10x Mar 21, 2024
2d4af2f
Extract the last cmp function and clean up naming.
macklin-10x Mar 21, 2024
17cd148
Remove the intermediate transformation but preserve existing variable…
macklin-10x Mar 22, 2024
279fe96
Adjust ref_start calculation to see if it makes a difference.
macklin-10x Mar 22, 2024
f2f2e12
Add missing mutations where we needed to update ref_start.
macklin-10x Mar 22, 2024
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3 changes: 1 addition & 2 deletions enclone_args/src/read_json.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -142,8 +142,7 @@ fn process_json_annotation(
// Reannotate.
if reannotate || ctl.gen_opt.reprod {
let x = DnaString::from_dna_string(&ann.sequence);
let mut ann1 = Vec::<Annotation>::new();
annotate_seq(&x, refdata, &mut ann1, true, false, true);
let mut ann1 = annotate_seq(&x, refdata, true, false, true);

// If there are multiple V segment alignments, possibly reduce to just one.

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