Code

fix: refactor csq analysis code#599

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Merged

tedil merged 38 commits intomainvarfish-org/mehari:mainfrom refactor-csq-c-and-pvarfish-org/mehari:refactor-csq-c-and-pCopy head branch name to clipboardNov 19, 2024

+1,205-707

Commits

Commits on Nov 4, 2024

• chore: refactor csq analysis code

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  9eb5000

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• more refactoring + move *_inframe_deletion detection to var_c (from var_p)

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  aa23589

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Commits on Nov 5, 2024

• update cargo lock

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  7bbe60a

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• alias BitFlags<Consequence> to Consequences

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  60811b1

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• undo: move inframedeletion to var_c (from var_p)

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  40c4b2c

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• lints

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  dccb09e

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• if let instead of match

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  b97b650

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• fix gained vs lost typo

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  5504862

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• remove multiple intron_start matches

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  0f71645

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• move intron_start check out of fn

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• don't overwrite previous consequences, union instead

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  5a80949

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• update cargo lock

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  ebdbd51

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• lint

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  81e8e2f

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Commits on Nov 6, 2024

• check for StopRetained based on DelIns length agreement with loc edit

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  68fef4b

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Commits on Nov 12, 2024

• merge origin/dev

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  d41d205

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• consider feature elongation

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  87d9f13

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• re-check start codon modifications

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  5cad620

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• use cmp and match

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  e44ee30

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• re-establish accidentally deleted inframedeletion csq

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  68d9fb4

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• remove superfluous prefix

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  31bffd6

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• account for cds change not starting at 1

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  91d6c0e

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• extract has_stop method

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  a110015

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• only undo stoplost when stopretained

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  c14f746

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• fix parentheses

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  29c8ef2

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• tidy up vep/snpeff comparison fixing code slightly

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  39c64d9

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• add specific test for vep reporting coding_sequence_variant only

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  e6be328

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Commits on Nov 14, 2024

• detangle intronic and exonic variant csq logic

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  bd69c9e

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• move more exon specific code into analyze_exonic_variant

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  968cbb4

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• update snapshots

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  a80e336

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Commits on Nov 15, 2024

• be a bit more careful when it comes to frameshifts

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  13d7a4e

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• uncomment last change for now

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  0259fad

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Commits on Nov 18, 2024

• move fs*2 handling to special case function

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  ec20820

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• clippy lint

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  cdc4e77

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• update comment

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  0d481e2

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• be more strict regarding start_retained

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  9837b9a

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• add todo regarding other cases (e.g. ins)

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  536bc7e

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• added testcase for vep←→ mehari disagreement cases

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  b62d629

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• added testcase for vep←→ mehari disagreement cases

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