Support chromosome synonyms in breakends #1064

nuno-agostinho · 2024-01-25T12:40:52Z

Support chromosome synonyms in breakends
- Requires VEP setting up the new $CHROMOSOME_SYNONYMS global variable in Fix chromosome synonyms for breakends and custom annotation ensembl-vep#1589
Fix breakends getting more features than they should by using the correct feature slice
Fix slices in unit tests

nuno-agostinho added 2 commits January 25, 2024 12:37

Support chromosome synonyms in breakends

9206bfa

Fix getting whole slice instead of feature slice

e81ec1f

nuno-agostinho mentioned this pull request Jan 25, 2024

Fix chromosome synonyms for breakends and custom annotation Ensembl/ensembl-vep#1589

Merged

nuno-agostinho added 2 commits January 25, 2024 15:33

Fix breakend alternative allele when in the end of ALT

5a5f56c

Fix slice in unit tests

09af2ba

nuno-agostinho marked this pull request as ready for review January 25, 2024 18:21

nakib103 self-requested a review January 29, 2024 09:34

nuno-agostinho assigned nakib103 Jan 29, 2024

nakib103 merged commit 423a7d7 into Ensembl:postreleasefix/112 Feb 6, 2024
1 check passed

nuno-agostinho deleted the fix/chr-sys-breakends branch February 6, 2024 16:35

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