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feat: update of dockerfile to use more secure image; #1546

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feat: update of dockerfile to use more secure image; #1546

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Commits on Dec 7, 2022

  1. Return features impacted by BND variants

    @nuno-agostinho
    nuno-agostinho committed Dec 7, 2022
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Commits on Apr 13, 2023

  1. Merge branch 'postreleasefix/109' into add/bnd-support

    @nuno-agostinho
    nuno-agostinho committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. Allow min_max regions per chromosome

    @nuno-agostinho
    nuno-agostinho committed Apr 14, 2023
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  2. Minor changes

    @nuno-agostinho
    nuno-agostinho committed Apr 14, 2023
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Commits on Apr 17, 2023

  1. Delete reg dba when done (Ensembl#1396)

    @nakib103
    nakib103 authored Apr 17, 2023
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  2. Delete reg dba when done (Ensembl#1396)

    @nakib103
    nakib103 authored Apr 17, 2023
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Commits on Apr 18, 2023

  1. Allow multiple vep and vcf config with one-to-one relationship

    @nakib103
    nakib103 committed Apr 18, 2023
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  2. Support breakend described in INFO field

    @nuno-agostinho
    nuno-agostinho committed Apr 18, 2023
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  3. Detect newer BND alternative allele format in VCF

    @nuno-agostinho
    nuno-agostinho committed Apr 18, 2023
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  4. Print BND alternative allele in output (if available)

    @nuno-agostinho
    nuno-agostinho committed Apr 18, 2023
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Commits on Apr 19, 2023

  1. Added support for multiple output dir

    @nakib103
    nakib103 committed Apr 19, 2023
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  2. Updated some comments in the code

    @nakib103
    nakib103 committed Apr 19, 2023
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  3. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed Apr 19, 2023
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  4. Fix unit tests and add breakend examples

    @nuno-agostinho
    nuno-agostinho committed Apr 19, 2023
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  5. Keep output for vcf workflow

    @nakib103
    nakib103 committed Apr 19, 2023
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  6. Fix unit tests

    @nuno-agostinho
    nuno-agostinho authored Apr 19, 2023
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  7. Avoid experimental warnings

    @nuno-agostinho
    nuno-agostinho authored Apr 19, 2023
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Commits on Apr 20, 2023

  1. Fix unknown chromosome in features from unit tests

    @nuno-agostinho
    nuno-agostinho committed Apr 20, 2023
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  2. Further fix unit tests

    @nuno-agostinho
    nuno-agostinho committed Apr 20, 2023
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  3. Support csi indexing

    @nakib103
    nakib103 committed Apr 20, 2023
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  4. More verbose extension matching

    @nakib103
    nakib103 committed Apr 20, 2023
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Commits on Apr 21, 2023

  1. Integrate SV Overlap plugin features

    @nuno-agostinho
    nuno-agostinho committed Apr 21, 2023
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Commits on Apr 24, 2023

  1. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed Apr 24, 2023
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Commits on Apr 26, 2023

  1. Fix using wrong variables

    @nuno-agostinho
    nuno-agostinho committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. Fix SO term comparison

    @nuno-agostinho
    nuno-agostinho committed Apr 27, 2023
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  2. Improve docs on overlap_cutoff

    @nuno-agostinho
    nuno-agostinho committed Apr 27, 2023
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  3. Fix unit tests

    @nuno-agostinho
    nuno-agostinho committed Apr 27, 2023
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Commits on May 2, 2023

  1. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed May 2, 2023
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Commits on May 19, 2023

  1. There can be dot in vcf file name

    @nakib103
    nakib103 committed May 19, 2023
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Commits on May 24, 2023

  1. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed May 24, 2023
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Commits on May 25, 2023

  1. Get ref allele from phenotype feature attrib

    @dglemos
    dglemos committed May 25, 2023
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Commits on Jun 2, 2023

  1. Merge pull request Ensembl#1423 from dglemos/ENSVAR_5773 

    Clinical significance - compare ref alleles
    @nakib103
    nakib103 authored Jun 2, 2023
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  2. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed Jun 2, 2023
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  3. Update dump VEP directories (Ensembl#1394) 

    * Update dump dir for DumpVEP pipeline

* Fix syntax

* Fix function name

* Update QC step

* Update distribute step

* Fix dir string

* Fix distribute dir for bacteria
    @nakib103
    nakib103 authored Jun 2, 2023
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Commits on Jun 5, 2023

  1. Update refseq stable id only when undefined

    @nakib103
    nakib103 committed Jun 5, 2023
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Commits on Jun 14, 2023

  1. Merge branch 'postreleasefix/110'

    @dglemos
    dglemos committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. Merge branch 'postreleasefix/110'

    @nakib103
    nakib103 committed Jun 15, 2023
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Commits on Jun 19, 2023

  1. Merge branch 'postreleasefix/110'

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 19, 2023
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  2. Branch name changed to main

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 19, 2023
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  3. Merge branch 'postreleasefix/110' into add/bnd-support

    @nuno-agostinho
    nuno-agostinho authored Jun 19, 2023
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  4. Fix git merge changes

    @nuno-agostinho
    nuno-agostinho authored Jun 19, 2023
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  5. Merge branch 'postreleasefix/110'

    @nuno-agostinho
    nuno-agostinho committed Jun 19, 2023
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Commits on Jun 20, 2023

  1. Fix class SO term for breakends

    @nuno-agostinho
    nuno-agostinho authored Jun 20, 2023
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  2. Merge branch 'postreleasefix/110' into add/SV-overlap

    @nuno-agostinho
    nuno-agostinho authored Jun 20, 2023
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  3. Fix unit tests

    @nuno-agostinho
    nuno-agostinho committed Jun 20, 2023
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  4. Merge branch 'postreleasefix/110' 

    Merging pull request "Print only file name as gff/gtf source Ensembl#1413"
    Gurpreet Singh Ghattaoraya committed Jun 20, 2023
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  5. Merge branch 'postreleasefix/110'

    @nuno-agostinho
    nuno-agostinho committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. Improve regex for validation of alternative alleles

    @nuno-agostinho
    nuno-agostinho authored Jun 21, 2023
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  2. Avoid nested routines

    @nuno-agostinho
    nuno-agostinho authored Jun 21, 2023
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  3. Update class SO term to chromosome_breakpoint

    @nuno-agostinho
    nuno-agostinho authored Jun 21, 2023
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Commits on Jun 26, 2023

  1. quick fix (Ensembl#1441)

    @olaaustine
    olaaustine authored Jun 26, 2023
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  2. Return overlap_percentage for exact matches

    @nuno-agostinho
    nuno-agostinho authored Jun 26, 2023
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  3. Fix overlap_percentage for exact matches

    @nuno-agostinho
    nuno-agostinho authored Jun 26, 2023
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  4. Fixed consequences for indels when shift_3prime is enabled for all in… 

    …puts
    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 26, 2023
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  5. Remove duplicated function

    @nuno-agostinho
    nuno-agostinho committed Jun 26, 2023
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  6. Fix overlap definition based on

    @nuno-agostinho
    nuno-agostinho committed Jun 26, 2023
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  7. Merge branch 'postreleasefix/111' into add/SV-overlap

    @nuno-agostinho
    nuno-agostinho authored Jun 26, 2023
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  8. Fix unit tests

    @nuno-agostinho
    nuno-agostinho authored Jun 26, 2023
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  9. Update unit tests

    @nuno-agostinho
    nuno-agostinho authored Jun 26, 2023
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  10. Fixed test cases for uploaded_allele as a flag

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 26, 2023
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  11. Avoid calculating overlap for breakpoints

    @nuno-agostinho
    nuno-agostinho committed Jun 26, 2023
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  12. Update modules/Bio/EnsEMBL/VEP/Parser.pm 

    Skipping SVs while checking for allele string

Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @likhitha-surapaneni @nuno-agostinho
    likhitha-surapaneni and nuno-agostinho authored Jun 26, 2023
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  13. Minor fix

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 26, 2023
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  14. Fix issues with unit tests

    @nuno-agostinho
    nuno-agostinho committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. Fix missing parameter on unit tests

    @nuno-agostinho
    nuno-agostinho committed Jun 27, 2023
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  2. remove blank line 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  3. use null instead of string 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  4. use null instead of string 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  5. fix the case where no index is not given 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  6. remove params from modules 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  7. remove blank line 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jun 27, 2023
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  8. refactor split vcf module

    @nakib103
    nakib103 committed Jun 27, 2023
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  9. Create output dir before moving

    @nakib103
    nakib103 committed Jun 27, 2023
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  10. Added unit tests for uploaded_allele flag

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 27, 2023
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  11. Remove many-to-many scenario altogether

    @nakib103
    nakib103 committed Jun 27, 2023
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  12. Fix custom headers warning in unit tests

    @nuno-agostinho
    nuno-agostinho committed Jun 27, 2023
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  13. remove unnecessary params and if branches

    @nakib103
    nakib103 committed Jun 27, 2023
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  14. fix typo

    @nakib103
    nakib103 committed Jun 27, 2023
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  15. convert non-absolute output dir path

    @nakib103
    nakib103 committed Jun 27, 2023
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  16. Revert overlap flag check

    @nuno-agostinho
    nuno-agostinho authored Jun 27, 2023
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  17. Fixing test cases

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. Minor fix

    @likhitha-surapaneni
    likhitha-surapaneni committed Jun 28, 2023
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  2. Merge pull request Ensembl#1407 from nuno-agostinho/add/SV-overlap

    @nuno-agostinho
    nuno-agostinho authored Jun 28, 2023
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  3. Merge pull request Ensembl#1399 from nuno-agostinho/add/bnd-support

    @nuno-agostinho
    nuno-agostinho authored Jun 28, 2023
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  4. Merge pull request Ensembl#1444 from likhitha-surapaneni/fix-uploaded… 

    …-allele
    @nuno-agostinho
    nuno-agostinho authored Jun 28, 2023
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  5. Minor fix for default values

    @nuno-agostinho
    nuno-agostinho committed Jun 28, 2023
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  6. Merge pull request Ensembl#1398 from nakib103/nxf_from_pipeline

    @nuno-agostinho
    nuno-agostinho authored Jun 28, 2023
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Commits on Jun 29, 2023

  1. bugfix: many-to-one situation; stop channeling output_dir

    @nakib103
    nakib103 committed Jun 29, 2023
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Commits on Jul 3, 2023

  1. flow vep_config from run_vep 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jul 3, 2023
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  2. take in vep_config from run_vep 

    Co-authored-by: Nuno Agostinho <nuno@ebi.ac.uk>
    @nakib103 @nuno-agostinho
    nakib103 and nuno-agostinho authored Jul 3, 2023
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Commits on Jul 4, 2023

  1. Fix one-to-many situation

    @nakib103
    nakib103 committed Jul 4, 2023
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  2. Merge pull request Ensembl#1448 from nakib103/nxf_from_pipeline

    @nuno-agostinho
    nuno-agostinho authored Jul 4, 2023
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Commits on Jul 7, 2023

  1. Ignore alternative allele when checking VCF format

    @nuno-agostinho
    nuno-agostinho committed Jul 7, 2023
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  2. Avoid warning regarding comma usage in qw

    @nuno-agostinho
    nuno-agostinho committed Jul 7, 2023
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  3. Support N as alternative allele (used in telomere breakends)

    @nuno-agostinho
    nuno-agostinho committed Jul 7, 2023
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  4. Improve SV type detection and add more skipped variants to skipped_va… 

    …riants_log
    @nuno-agostinho
    nuno-agostinho committed Jul 7, 2023
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Commits on Jul 12, 2023

  1. Revert "Update refseq stable id only when undefined" 

    This reverts commit f3829f7.
    @nakib103
    nakib103 committed Jul 12, 2023
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  2. Allow non rna- prefix in transcript stable id

    @nakib103
    nakib103 committed Jul 12, 2023
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  3. Put a end-of-line condition in the regex for better match

    @nakib103
    nakib103 committed Jul 12, 2023
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  4. Extra condition to check MT transcripts

    @nakib103
    nakib103 committed Jul 12, 2023
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Commits on Jul 17, 2023

  1. Merge pull request Ensembl#1451 from nuno-agostinho/fix/sv-alt-vcf 

    Avoid error for alternative allele in first line of VCF input
    @nakib103
    nakib103 authored Jul 17, 2023
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Commits on Jul 18, 2023

  1. Fix Docker build process

    @nuno-agostinho
    nuno-agostinho authored Jul 18, 2023
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  2. Add tag for manual run

    @nuno-agostinho
    nuno-agostinho authored Jul 18, 2023
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  3. Merge pull request Ensembl#1454 from nuno-agostinho/fix/gh-actions-do… 

    …cker

Fix Docker build process
    @likhitha-surapaneni
    likhitha-surapaneni authored Jul 18, 2023
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Commits on Jul 24, 2023

  1. Update dockerfile for ubuntu 22.04

    @nakib103
    nakib103 committed Jul 24, 2023
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  2. Fix Dockerfile context

    @nuno-agostinho
    nuno-agostinho authored Jul 24, 2023
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  3. Merge pull request Ensembl#1462 from nuno-agostinho/fix/dockerfile-co… 

    …ntext

Fix Dockerfile context
    @likhitha-surapaneni
    likhitha-surapaneni authored Jul 24, 2023
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  4. Avoid Docker layer caching

    @nuno-agostinho
    nuno-agostinho authored Jul 24, 2023
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  5. Merge pull request Ensembl#1463 from nuno-agostinho/fix/dockerfile-co… 

    …ntext

Avoid Docker layer caching
    @likhitha-surapaneni
    likhitha-surapaneni authored Jul 24, 2023
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  6. Remove test sed expressions

    @nakib103
    nakib103 committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. Symlink python to python2

    @nakib103
    nakib103 committed Jul 25, 2023
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Commits on Aug 3, 2023

  1. Avoid smartmatch (Ensembl#1461)

    @nuno-agostinho
    nuno-agostinho authored Aug 3, 2023
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Commits on Aug 7, 2023

  1. Avoid annotating skipped variants

    @nuno-agostinho
    nuno-agostinho authored Aug 7, 2023
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Commits on Aug 8, 2023

  1. Merge pull request Ensembl#1464 from nakib103/ubuntu_python2 

    Docker: update ubuntu version latest LTS (22.04)
    @likhitha-surapaneni
    likhitha-surapaneni authored Aug 8, 2023
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Commits on Aug 15, 2023

  1. Fix web VEP input format detection

    @nuno-agostinho
    nuno-agostinho committed Aug 15, 2023
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  2. Remind to edit public-plugins JS code

    @nuno-agostinho
    nuno-agostinho committed Aug 15, 2023
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  3. Remove input format detection from VEP

    @nuno-agostinho
    nuno-agostinho committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. Merge pull request Ensembl#1473 from nuno-agostinho/fix/custom-annot-… 

    …skip-vars

Avoid custom annotation of skipped variants
    @nakib103
    nakib103 authored Aug 16, 2023
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Commits on Aug 18, 2023

  1. Parse mobile element insertion/deletion

    @nuno-agostinho
    nuno-agostinho committed Aug 18, 2023
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  2. Fix formatting detection issues

    @nuno-agostinho
    nuno-agostinho committed Aug 18, 2023
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Commits on Aug 25, 2023

  1. Remove clinvar ref allele

    @dglemos
    dglemos committed Aug 25, 2023
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  2. Add option to report zygozity

    @dglemos
    dglemos committed Aug 25, 2023
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Commits on Aug 29, 2023

  1. Add new option to constants

    @dglemos
    dglemos committed Aug 29, 2023
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  2. Add a test

    @dglemos
    dglemos committed Aug 29, 2023
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  3. More tests

    @dglemos
    dglemos committed Aug 29, 2023
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Commits on Aug 30, 2023

  1. Fix Haplo_Runner test

    @dglemos
    dglemos committed Aug 30, 2023
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  2. Add more tests

    @dglemos
    dglemos committed Aug 30, 2023
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  3. Fix order

    @dglemos
    dglemos committed Aug 30, 2023
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  4. Parse END field in Manta breakend variants

    @nuno-agostinho
    nuno-agostinho committed Aug 30, 2023
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  5. Fix unit tests

    @nuno-agostinho
    nuno-agostinho committed Aug 30, 2023
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  6. Add mobile element unit tests

    @nuno-agostinho
    nuno-agostinho committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. Allow output dir to be a channel

    @nakib103
    nakib103 committed Aug 31, 2023
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Commits on Sep 1, 2023

  1. If output_dir is channel leave as it is

    @nakib103
    nakib103 committed Sep 1, 2023
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Commits on Sep 5, 2023

  1. Copy-edit code

    @nuno-agostinho
    nuno-agostinho authored Sep 5, 2023
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  2. Merge pull request Ensembl#1477 from nuno-agostinho/fix/web-vep-input… 

    …-format

Fix web VEP input format detection
    @nakib103
    nakib103 authored Sep 5, 2023
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Commits on Sep 6, 2023

  1. Update more splits

    @nakib103
    nakib103 committed Sep 6, 2023
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  2. Remove non-existant function call

    @nakib103
    nakib103 committed Sep 6, 2023
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  3. Added wrong files in prev commit

    @nakib103
    nakib103 committed Sep 6, 2023
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Commits on Sep 11, 2023

  1. Merge pull request Ensembl#1493 from nakib103/fix_nextflow

    @nuno-agostinho
    nuno-agostinho authored Sep 11, 2023
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  2. Parse breakends as multiple alternative alleles

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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  3. Move breakend parsing to ensembl-variation

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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  4. Clean breakend code

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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  5. Parse Manta breakends in ensembl-vep

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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  6. Fix wrong allele string for Manta results

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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  7. Fix unit tests

    @nuno-agostinho
    nuno-agostinho committed Sep 11, 2023
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Commits on Sep 14, 2023

  1. Avoid matching breakpoints with SNPs in exact mode

    @nuno-agostinho
    nuno-agostinho committed Sep 14, 2023
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  2. Trim extra whitespaces of warning messages for skipped variants

    @nuno-agostinho
    nuno-agostinho committed Sep 14, 2023
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  3. Fix skipping all subsequent SVs after skipping one

    @nuno-agostinho
    nuno-agostinho committed Sep 14, 2023
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  4. Warn when skipping any non-supported SV type

    @nuno-agostinho
    nuno-agostinho committed Sep 14, 2023
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  5. Match by same variant type only with custom VCF

    @nuno-agostinho
    nuno-agostinho committed Sep 14, 2023
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Commits on Sep 18, 2023

  1. Avoid getting breakends if method is not available (example, for non-… 

    …SVs)
    @nuno-agostinho
    nuno-agostinho committed Sep 18, 2023
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  2. Avoid getting breakends if not available

    @nuno-agostinho
    nuno-agostinho committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. Fix breakend parsing from INFO field

    @nuno-agostinho
    nuno-agostinho committed Sep 19, 2023
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  2. Avoid error regarding unblessed objects in haplo

    @nuno-agostinho
    nuno-agostinho committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Fix typo

    @nakib103
    nakib103 committed Sep 20, 2023
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  2. Added unit test

    @nakib103
    nakib103 committed Sep 20, 2023
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  3. Shorten the lines

    @nakib103
    nakib103 committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. Compare samples

    @dglemos
    dglemos committed Sep 21, 2023
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Commits on Sep 22, 2023

  1. Fix check and add tests

    @dglemos
    dglemos committed Sep 22, 2023
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  2. Merge pull request Ensembl#1490 from dglemos/add/option_individual_zyg

    @nuno-agostinho
    nuno-agostinho authored Sep 22, 2023
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  3. Add correct breakend reference to breakpoints

    @nuno-agostinho
    nuno-agostinho committed Sep 22, 2023
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  4. Support single breakends, such as .N

    @nuno-agostinho
    nuno-agostinho committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. Improve unit tests

    @nuno-agostinho
    nuno-agostinho committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Merge pull request Ensembl#1496 from nuno-agostinho/improve-bnd 

    Report consequences for each breakend (e112)
    @likhitha-surapaneni
    likhitha-surapaneni authored Sep 26, 2023
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Commits on Sep 27, 2023

  1. Run VEP with SV IDs (Ensembl#1478) 

    * Search database by SV ID

* Add SV ID unit tests

* Generalise max_sv_size limit to all input formats

* Fix unit tests

* Show warning in REST

* Fix unit tests

* Fix VCF output for skipped variants (non-VCF input)
    @nuno-agostinho
    nuno-agostinho authored Sep 27, 2023
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Commits on Sep 28, 2023

  1. git merge postreleasefix/111 after conflicts resolved

    @dglemos
    dglemos committed Sep 28, 2023
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  2. Merge branch 'postreleasefix/111' into fix/custom-skipping

    @nuno-agostinho
    nuno-agostinho authored Sep 28, 2023
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Commits on Sep 29, 2023

  1. Merge pull request Ensembl#1498 from nuno-agostinho/fix/custom-skipping 

    Fix custom annotation of breakends and non-supported SVs (exact mode)
    @nakib103
    nakib103 authored Sep 29, 2023
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  2. Resolve merge conflict

    @nakib103
    nakib103 committed Sep 29, 2023
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  3. Merge branch 'postreleasefix/111' into fix/manta-BND-end

    @nuno-agostinho
    nuno-agostinho authored Sep 29, 2023
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  4. Merge branch 'postreleasefix/111' into add/vcf-mobile-elements

    @nuno-agostinho
    nuno-agostinho authored Sep 29, 2023
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  5. Merge pull request Ensembl#1491 from nuno-agostinho/fix/manta-BND-end 

    Parse END field in Manta breakend variants
    @nakib103
    nakib103 authored Sep 29, 2023
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  6. Resolve merge conflict

    @nakib103
    nakib103 committed Sep 29, 2023
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Commits on Oct 2, 2023

  1. Custom annotations: summary statistics + filter by number of records (E… 

    …nsembl#1470)

* Extend all --custom options available to bigwig files

* Add max number of records and summary statistics to custom annotations

* Fix calculation of number of records

* Fix unit tests

* Fix unit tests

* Fix num_records=0 being ignored

* Check for invalid options in custom usage

* Create scores for BED and bigwig files (even with coords=1)

* Allow using summary statistics with other formats (off by default)

* Improve error message

* Fix not adding ellipsis when not calculating statistics

* Bug fixes for other formats

* Add unit tests for BED and BigWig files

* Fix VCF scores

* Fix issues with VCF with no scores

* Improve unit tests

* Fix JSON output

* Change default to not calculate summary statistics

* Code cleanup

* Fix unit tests
    @nuno-agostinho
    nuno-agostinho authored Oct 2, 2023
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  2. Merge branch 'postreleasefix/111'

    @dglemos
    dglemos committed Oct 2, 2023
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Commits on Oct 3, 2023

  1. Merge pull request Ensembl#1487 from dglemos/revert/pr_1423 

    Clinical significance - remove clinvar ref allele check
    @jamie-m-a
    jamie-m-a authored Oct 3, 2023
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  2. Merge branch 'postreleasefix/111'

    @jamie-m-a
    jamie-m-a committed Oct 3, 2023
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  3. Resolve conflict

    @nakib103
    nakib103 committed Oct 3, 2023
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Commits on Oct 5, 2023

  1. Merge branch 'postreleasefix/111' into add/vcf-mobile-elements

    @nuno-agostinho
    nuno-agostinho authored Oct 5, 2023
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Commits on Oct 9, 2023

  1. Improve warning message

    @nuno-agostinho @likhitha-surapaneni
    nuno-agostinho authored and likhitha-surapaneni committed Oct 9, 2023
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  2. Avoid printing warnings when running unit tests

    @nuno-agostinho @likhitha-surapaneni
    nuno-agostinho authored and likhitha-surapaneni committed Oct 9, 2023
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  3. Merge branch 'postreleasefix/111'

    @likhitha-surapaneni
    likhitha-surapaneni committed Oct 9, 2023
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  4. Merge pull request Ensembl#1429 from nakib103/fix_cache

    @nuno-agostinho
    nuno-agostinho authored Oct 9, 2023
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  5. Merge branch 'postreleasefix/111'

    @nuno-agostinho
    nuno-agostinho committed Oct 9, 2023
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  6. Fix unit tests

    @nuno-agostinho
    nuno-agostinho authored Oct 9, 2023
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Commits on Oct 12, 2023

  1. Update VCF.pm

    @nuno-agostinho
    nuno-agostinho authored Oct 12, 2023
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  2. Merge pull request Ensembl#1513 from nuno-agostinho/fix/main-tests 

    Fix unit tests in main branch
    @nakib103
    nakib103 authored Oct 12, 2023
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Commits on Oct 13, 2023

  1. Fetch chromosome synonyms from cache in offline mode

    @dglemos
    dglemos committed Oct 13, 2023
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Commits on Oct 15, 2023

  1. ignore blank lines in the config.ini 

    currently these generate ugly warnings. I use space and comments in the config file for readability
    @dbolser
    Dan Bolser authored and dbolser committed Oct 15, 2023
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  2. Update INSTALL.pl 

    Making CLI options mirror variables... for some reason.
    @dbolser
    dbolser committed Oct 15, 2023
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Commits on Oct 16, 2023

  1. Merge pull request Ensembl#1522 from dbolser/postreleasefix/111

    @nuno-agostinho
    nuno-agostinho authored Oct 16, 2023
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  2. Merge branch 'postreleasefix/111'

    @nuno-agostinho
    nuno-agostinho committed Oct 16, 2023
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  3. Merge pull request Ensembl#1521 from dglemos/fix_hgvsg_use_accession 

    --hgvsg_use_accession to fetch chromosome synonyms from cache in offline mode
    @likhitha-surapaneni
    likhitha-surapaneni authored Oct 16, 2023
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  4. Merge pull request Ensembl#1523 from dbolser/patch-3 

    Update INSTALL.pl
    @likhitha-surapaneni
    likhitha-surapaneni authored Oct 16, 2023
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  5. Merge branch 'postreleasefix/111'

    @likhitha-surapaneni
    likhitha-surapaneni committed Oct 16, 2023
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Commits on Oct 18, 2023

  1. Fix web distribute dir for Dump VEP (Ensembl#1525)

    @nakib103
    nakib103 authored Oct 18, 2023
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  2. Merge branch 'postreleasefix/111'

    @dglemos
    dglemos committed Oct 18, 2023
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  3. Merge pull request Ensembl#1481 from nuno-agostinho/add/vcf-mobile-el… 

    …ements

Parse mobile element insertion/deletion
    @olaaustine
    olaaustine authored Oct 18, 2023
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  4. merging conflicts

    @olaaustine
    olaaustine committed Oct 18, 2023
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  5. Resolving residual commit merge conflict lines

    @olaaustine
    olaaustine committed Oct 18, 2023
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Commits on Oct 19, 2023

  1. Patching all test DBs to 112

    @jamie-m-a
    jamie-m-a committed Oct 19, 2023
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  2. Fix merge conflict changes in main

    @nuno-agostinho
    nuno-agostinho authored Oct 19, 2023
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  3. Fix CNV unit tests

    @nuno-agostinho
    nuno-agostinho committed Oct 19, 2023
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  4. Merge pull request Ensembl#1528 from nuno-agostinho/fix/unit-tests 

    Fix conflicting changes in main
    @olaaustine
    olaaustine authored Oct 19, 2023
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  5. Updating VEP version

    @jamie-m-a
    jamie-m-a committed Oct 19, 2023
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  6. Merge pull request Ensembl#1527 from jamie-m-a/DB-patching 

    Patching all test DBs to 112
    @likhitha-surapaneni
    likhitha-surapaneni authored Oct 19, 2023
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Commits on Oct 20, 2023

  1. Merge pull request Ensembl#1531 from jamie-m-a/update-version 

    Updating VEP version
    @likhitha-surapaneni
    likhitha-surapaneni authored Oct 20, 2023
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  2. Fix command plugin path

    @nuno-agostinho
    nuno-agostinho committed Oct 20, 2023
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  3. Lookahead to avoid stripping the directory path if finishing with /

    @nuno-agostinho
    nuno-agostinho committed Oct 20, 2023
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  4. Avoid redundant code

    @nuno-agostinho
    nuno-agostinho committed Oct 20, 2023
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Commits on Oct 23, 2023

  1. Fix Docker build badge

    @nuno-agostinho
    nuno-agostinho authored Oct 23, 2023
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  2. Merge pull request Ensembl#1538 from nuno-agostinho/fix/docker-badge 

    Fix Docker build badge
    @likhitha-surapaneni
    likhitha-surapaneni authored Oct 23, 2023
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Commits on Nov 2, 2023

  1. feat: update of dockerfile to use more secure image; 

    the base image has been updates to Ubuntu 23.04 as 18.04 is End-of-Life
the ubuntu-pacakges.txt file is no longer being recovered, these packages are explicitly installed
python packages have been updated to address vulnerabilities
plugins which rely on Python2 have been excluded as this version reached End-of-Life 01JAN2020

included instructions on installing the non-canonical LOFTEE plugin on lines 78-84 & 226-233, these
can be excluded if LOFTEE is not going to be used
    @mvforster
    mvforster committed Nov 2, 2023
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  2. Merge pull request Ensembl#1535 from nuno-agostinho/fix/command-plugi… 

    …n-path

Fix plugin path in command line output
    @nakib103
    nakib103 authored Nov 2, 2023
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Commits on Nov 3, 2023

  1. Restrain using latest DBD::mysql version

    @nakib103 @likhitha-surapaneni
    nakib103 authored and likhitha-surapaneni committed Nov 3, 2023
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Commits on Nov 17, 2023

  1. Deterministic order for software versions in header (Ensembl#1545) 

    * Deterministic order for software versions

* Deterministic order for software versions
    @likhitha-surapaneni
    likhitha-surapaneni authored Nov 17, 2023
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Commits on Dec 5, 2023

  1. chore: rebasing the forked project to postreleasefix/112

    @diegomscoelho @mvforster
    diegomscoelho authored and mvforster committed Dec 5, 2023
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  2. chore: rebase fork to postreleasefix/112 

    rebasing the fork so that the pull request can be applied to the correct branch
    @nakib103 @mvforster
    nakib103 authored and mvforster committed Dec 5, 2023
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  3. Fix conflict

    @nakib103 @mvforster
    nakib103 authored and mvforster committed Dec 5, 2023
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  4. chore: fix conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 5, 2023
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  5. Fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 5, 2023
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  6. chore: fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 5, 2023
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Commits on Dec 12, 2023

  1. chore: fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  2. chore: fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  3. chore: fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  4. Detect newer BND alternative allele format in VCF

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  5. Fix git merge changes

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  6. Improve regex for validation of alternative alleles

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  7. Return features impacted by BND variants

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  8. chore: fix rebase conflicts

    @nuno-agostinho @mvforster
    nuno-agostinho authored and mvforster committed Dec 12, 2023
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  9. feat: update of dockerfile to use more secure image; 

    the base image has been updates to Ubuntu 23.04 as 18.04 is End-of-Life
the ubuntu-pacakges.txt file is no longer being recovered, these packages are explicitly installed
python packages have been updated to address vulnerabilities
plugins which rely on Python2 have been excluded as this version reached End-of-Life 01JAN2020

included instructions on installing the non-canonical LOFTEE plugin on lines 78-84 & 226-233, these
can be excluded if LOFTEE is not going to be used
    @mvforster
    mvforster committed Dec 12, 2023
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  10. Merge branch 'v110/updates' of github.com:mvforster/ensembl-vep into … 

    …v110/updates
    @mvforster
    mvforster committed Dec 12, 2023
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