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Handle SV in hypsipyle - #65

Merged

likhitha-surapaneni merged 61 commits into

Ensembl:dev-v2.0from

likhitha-surapaneni:feature/handle-sv

Nov 10, 2026

Merged

Handle SV in hypsipyle#65
likhitha-surapaneni merged 61 commits into
Ensembl:dev-v2.0from
likhitha-surapaneni:feature/handle-sv

Commits on Feb 17, 2026
- Add bcftools in setup
  likhitha-surapaneni
  committed
  5e4e2dd
- Add structural_variant query type
  likhitha-surapaneni
  committed
  6e52cec
- Add graphql schema for structural variants
  likhitha-surapaneni
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  f7524ea
- Add placeholder file model for structural variants
  likhitha-surapaneni
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  eff56e3
- Add logic to fetch sv from files
  likhitha-surapaneni
  committed
  785ba2d
Commits on Feb 18, 2026
- Modified code to create an index for first pass of variant search
  likhitha-surapaneni
  committed
  63e06c9
Commits on Mar 2, 2026
- Handle sv from single merged file
  likhitha-surapaneni
  committed
  7036ed5
Commits on Mar 3, 2026
- Modularised file_model classes
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  3cff596
- Formatting updates
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  c876c8a
- Formatting changes
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  70e8a48
- Added base_variant file
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  eae570f
Commits on Mar 31, 2026
- Added indexing script; logic for allele,allele_type
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  committed
  3a1d212
- Add functionality for allele prediction results
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  7c41f7c
- Minor cleanup
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  ef3fd01
Commits on Apr 28, 2026
- Implemented logic for structural variant and allele synonyms
  likhitha-surapaneni
  committed
  a9427fe
- Separated logic for index client
  likhitha-surapaneni
  committed
  5b27a13
- Added testing for SVs
  likhitha-surapaneni
  committed
  00d0b6f
- Added testing for SVs
  likhitha-surapaneni
  committed
  569eb89
Commits on May 11, 2026
- Restructuring code to support multiple sources for short variants
  likhitha-surapaneni
  committed
  1399a16
Commits on May 12, 2026
- Reorganised BaseFileClient and FileClient
  likhitha-surapaneni
  committed
  f8b99dc
Commits on Jun 10, 2026
- Added an example json
  likhitha-surapaneni
  committed
  4ed6fad
Commits on Jul 3, 2026
Commits on Jul 7, 2026
- chore: code cleanup and comments
  likhitha-surapaneni
  committed
  590adf1
- fix: changes to name, length, copy_number for structural_variant_allele
  likhitha-surapaneni
  committed
  5956ce1
Commits on Jul 15, 2026
- Fix name when ALLELE_NAME is not present but is symbolic; Fix allele_type when SVTYPE is not present but is symbolic
  likhitha-surapaneni
  committed
  f388a6c
- fix: add missing value for SV allele_type for CNV
  likhitha-surapaneni
  committed
  c43a1a2
Commits on Jul 16, 2026
- fix: reference length for insertion
  likhitha-surapaneni
  committed
  65ea1ed
- chore: Added Makefile for build automation and streamlined project setup
  likhitha-surapaneni
  committed
  eb1ad43
Commits on Jul 29, 2026
- feat: predicted_molecular_consequence for sv
  likhitha-surapaneni
  committed
  e007491
- feat: Handle spdi from file
  likhitha-surapaneni
  committed
  e55e7d5
Commits on Aug 3, 2026
- feat: normalise spdi
  likhitha-surapaneni
  committed
  c30191a
Commits on Aug 17, 2026
- fix: allele_type corrected when allele is symbolic
  likhitha-surapaneni
  committed
  a12a4bc
Commits on Aug 18, 2026
- Consolidated methods between parent and child classes
  likhitha-surapaneni
  committed
  947c024
Commits on Sep 1, 2026
- Fixed alternative_names calling self.name
  likhitha-surapaneni
  committed
  ca93a99
- Corrected gold_standard data for sv
  likhitha-surapaneni
  committed
  21b6e66
- Minor bug fix
  likhitha-surapaneni
  committed
  0867041
Commits on Sep 14, 2026
- fix: lengths for slice and length for SV
  likhitha-surapaneni
  committed
  485277c
- chore: added target for colima profile cleaning
  likhitha-surapaneni
  committed
  496085d
- chore: get_slice in respective child classes
  likhitha-surapaneni
  committed
  bef6e0e
- fix: CI tests
  likhitha-surapaneni
  committed
  658fedc
Commits on Sep 15, 2026
- chore: cleanup
  likhitha-surapaneni
  committed
  b93479a
- chore: added pre-commit hook
  likhitha-surapaneni
  committed
  69cce56
Commits on Sep 21, 2026
- Update common/file_model/structural_variant_allele.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  5cdaee3
- Update common/schemas/structural_variant.graphql
  
  likhitha-surapaneni
  and
  richysix
  authored
  0fe1704
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  1c3f242
- Update graphql_service/resolver/structural_variant_model.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  92cfac4
- Update common/file_model/structural_variant_allele.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  57cea16
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  3285e23
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  21e3a74
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  102eae8
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  974d824
- Update common/file_model/structural_variant_allele.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  569c246
- Update common/file_model/structural_variant_allele.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  761e841
- Update common/file_model/structural_variant.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  be80f49
- Update common/file_model/structural_variant_allele.py
  
  likhitha-surapaneni
  and
  richysix
  authored
  21329b5
Commits on Sep 28, 2026
- feat: restuructured get_allele_type for variant and variant_allele
  likhitha-surapaneni
  committed
  54567dd
- chore: added a target for pytest
  likhitha-surapaneni
  committed
  90148a1

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Commits on Sep 28, 2026