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feat: merge vardict and tnscope #1475

Merged
merged 322 commits into from
Oct 14, 2024
Merged

feat: merge vardict and tnscope #1475

merged 322 commits into from
Oct 14, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 11, 2024

  1. remove dbsnp from TNscope test

    @mathiasbio
    mathiasbio committed Jun 11, 2024
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Commits on Jun 14, 2024

  1. add gens functionality to tga

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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  2. add gens inputs

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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  3. add gens gnomad af to tga

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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  4. black

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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  6. fix

    @mathiasbio
    mathiasbio committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  3. fix

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  4. doc strings and named args

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  5. black

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  6. changelog

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  7. bug fix

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  8. fix

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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  9. lower padding

    @mathiasbio
    mathiasbio committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. add tumor purity adjustment to gens cov file

    @mathiasbio
    mathiasbio committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. typehints

    @mathiasbio
    mathiasbio committed Jun 19, 2024
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  2. black

    @mathiasbio
    mathiasbio committed Jun 19, 2024
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  3. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jun 19, 2024
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  4. fix merge conflicts

    @mathiasbio
    mathiasbio committed Jun 19, 2024
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  5. fix pytests

    @mathiasbio
    mathiasbio committed Jun 19, 2024
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Commits on Jun 28, 2024

  1. update purity adjustment formula

    @mathiasbio
    mathiasbio committed Jun 28, 2024
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  2. Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into … 

    …develop
    @mathiasbio
    mathiasbio committed Jun 28, 2024
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  3. merge develop

    @mathiasbio
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  4. m conflict

    @mathiasbio
    mathiasbio committed Jun 28, 2024
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  5. m conflict

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Commits on Jul 10, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  2. fix merge conflicts

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  3. fix bugs

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  4. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  5. solve merge conflicts

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 11, 2024
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  2. Merge branch 'deduplicate_with_umi' into replace_vardict_with_tnscope

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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  3. fix bug

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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  4. fix pytests

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 12, 2024
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  2. Merge branch 'deduplicate_with_umi' into replace_vardict_with_tnscope

    @mathiasbio
    mathiasbio committed Jul 12, 2024
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  3. changelog

    @mathiasbio
    mathiasbio committed Jul 12, 2024
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Commits on Jul 15, 2024

  1. adjust formula

    @mathiasbio
    mathiasbio committed Jul 15, 2024
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  2. add round

    @mathiasbio
    mathiasbio committed Jul 15, 2024
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Commits on Jul 22, 2024

  1. changelog black

    @mathiasbio
    mathiasbio committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. add dbsnp

    @mathiasbio
    mathiasbio committed Jul 23, 2024
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  2. fix wgs sampletype

    @mathiasbio
    mathiasbio committed Jul 23, 2024
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  3. fix dbsnp placement

    @mathiasbio
    mathiasbio committed Jul 23, 2024
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  4. code review

    @mathiasbio
    mathiasbio committed Jul 23, 2024
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  5. fix merge conflicts

    @mathiasbio
    mathiasbio committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. fix bug

    @mathiasbio
    mathiasbio committed Jul 24, 2024
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  2. float

    @mathiasbio
    mathiasbio committed Jul 24, 2024
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  3. comment out purity and ploidy adjustment

    @mathiasbio
    mathiasbio committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. adjust purity and ploidy

    @mathiasbio
    mathiasbio committed Jul 25, 2024
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  2. bug fix

    @mathiasbio
    mathiasbio committed Jul 25, 2024
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  3. remove purity and ploidy adjustment

    @mathiasbio
    mathiasbio committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. add fixmate and min mapq 20 to cnvkit pon workflow for consistency

    @mathiasbio
    mathiasbio committed Jul 26, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. new threads

    @mathiasbio
    mathiasbio committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. feat: extend bedfiles for CNV analysis (#1469) 

    ## Added
- padding of bed-regions for CNVkit to minimum 100 base
    @mathiasbio
    mathiasbio authored Jul 30, 2024
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  2. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  3. bug

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  4. review fixes

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  5. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  6. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  7. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  8. update from parent branch

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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  9. fix sort

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. fix bug

    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  2. revert to using bedtools

    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  3. fix

    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  4. return purity adjustment

    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  5. code review

    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  6. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Jul 31, 2024
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  7. merge conflict

    @mathiasbio
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Commits on Aug 1, 2024

  1. black

    @mathiasbio
    mathiasbio committed Aug 1, 2024
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  2. new purity and ploidy formula from PureCN

    @mathiasbio
    mathiasbio committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. merge pon repo

    @mathiasbio
    mathiasbio committed Aug 2, 2024
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  2. merge cnvkit to gens branch

    @mathiasbio
    mathiasbio committed Aug 2, 2024
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  3. black

    @mathiasbio
    mathiasbio committed Aug 2, 2024
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  4. fix pytests

    @mathiasbio
    mathiasbio committed Aug 2, 2024
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  5. black

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    mathiasbio committed Aug 2, 2024
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  6. Merge branch 'cnvkit_to_gens' of github.com:Clinical-Genomics/BALSAMI… 

    …C into cnvkit_to_gens
    @mathiasbio
    mathiasbio committed Aug 2, 2024
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  7. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
    mathiasbio committed Aug 2, 2024
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Commits on Aug 5, 2024

  1. fix reliability sonarcloud error

    @mathiasbio
    mathiasbio committed Aug 5, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Aug 5, 2024
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  3. fix code duplication

    @mathiasbio
    mathiasbio committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. test update samtools 1.20

    @mathiasbio
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Commits on Aug 8, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Aug 8, 2024
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  2. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

    @mathiasbio
    mathiasbio committed Aug 8, 2024
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  3. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
    @mathiasbio
    mathiasbio committed Aug 8, 2024
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  4. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

    @mathiasbio
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  5. Merge branch 'cnvkit_to_gens' of github.com:Clinical-Genomics/BALSAMI… 

    …C into cnvkit_to_gens
    @mathiasbio
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  6. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
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  7. restore samtools

    @mathiasbio
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Commits on Aug 9, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
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  2. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

    @mathiasbio
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  3. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
    @mathiasbio
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  4. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

    @mathiasbio
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  5. Merge branch 'cnvkit_to_gens' of github.com:Clinical-Genomics/BALSAMI… 

    …C into cnvkit_to_gens
    @mathiasbio
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  6. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
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  7. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  8. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  9. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
    @mathiasbio
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  10. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

    @mathiasbio
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  11. Merge branch 'cnvkit_to_gens' of github.com:Clinical-Genomics/BALSAMI… 

    …C into cnvkit_to_gens
    @mathiasbio
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  12. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
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  13. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
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  14. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

    @mathiasbio
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  15. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
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  16. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

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  17. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
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  18. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

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  19. Merge branch 'cnvkit_to_gens' of github.com:Clinical-Genomics/BALSAMI… 

    …C into cnvkit_to_gens
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  20. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
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  21. fix

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  22. fix

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  23. test

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  24. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
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  25. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

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  26. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
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  27. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

    @mathiasbio
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Commits on Aug 12, 2024

  1. cleaning up old code

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  2. clean up

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Commits on Aug 13, 2024

  1. add io test

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  2. add new test

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Commits on Aug 14, 2024

  1. add umi edit distance 1

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Commits on Aug 15, 2024

  1. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
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  2. Merge branch 'deduplicate_with_umi' into update_cnvkit_pons

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  3. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
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  4. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

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Commits on Aug 19, 2024

  1. increase threads

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  2. clean up

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Commits on Aug 20, 2024

  1. fix pytest

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  2. changelog

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  3. Merge branch 'cnvkit_to_gens' into replace_vardict_with_tnscope

    @mathiasbio
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  4. docs

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  5. bla

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  6. Merge branch 'replace_vardict_with_tnscope' of github.com:Clinical-Ge… 

    …nomics/BALSAMIC into replace_vardict_with_tnscope
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  7. black

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Commits on Aug 22, 2024

  1. add vardict back and merge with tnscope

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Commits on Aug 23, 2024

  1. add merge to annotate and filter

    @mathiasbio
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  2. fix

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  3. add vardict params back

    @mathiasbio
    mathiasbio committed Aug 23, 2024
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  4. fix

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  5. fix

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  6. fix

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  7. fix

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  8. fix

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  9. fix

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  10. fix

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  11. fix

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  12. fix

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  13. fix

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  14. fix

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Commits on Aug 26, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Aug 26, 2024
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  2. test

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  3. test

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  4. test

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Commits on Aug 27, 2024

  1. test

    @mathiasbio
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  2. test

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  3. test

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  4. test

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  5. fix

    @mathiasbio
    mathiasbio committed Aug 27, 2024
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  6. fix

    @mathiasbio
    mathiasbio committed Aug 27, 2024
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  7. refactor code

    @mathiasbio
    mathiasbio committed Aug 27, 2024
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  8. fix

    @mathiasbio
    mathiasbio committed Aug 27, 2024
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  9. fix

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  10. test

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Commits on Aug 28, 2024

  1. fix

    @mathiasbio
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  2. fix

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  3. fix

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  4. fix

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  5. fix

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  6. fix

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  7. fix

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  8. fix

    @mathiasbio
    mathiasbio committed Aug 28, 2024
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  9. update

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Commits on Aug 29, 2024

  1. replace picard with bcftools

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  2. fix

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    mathiasbio committed Aug 29, 2024
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  3. change LC

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  4. fix sort

    @mathiasbio
    mathiasbio committed Aug 29, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Aug 29, 2024
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  6. add threads

    @mathiasbio
    mathiasbio committed Aug 29, 2024
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  7. fix

    @mathiasbio
    mathiasbio committed Aug 29, 2024
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  8. fix vardict filter

    @mathiasbio
    mathiasbio committed Aug 29, 2024
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  9. fic

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  10. fix

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    mathiasbio committed Aug 29, 2024
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Commits on Sep 2, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Sep 2, 2024
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  2. fix rules

    @mathiasbio
    mathiasbio committed Sep 2, 2024
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  3. fix pytests

    @mathiasbio
    mathiasbio committed Sep 2, 2024
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  4. clean up

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  5. add tmp variables

    @mathiasbio
    mathiasbio committed Sep 2, 2024
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  6. black

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    mathiasbio committed Sep 2, 2024
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  7. clean up

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Commits on Sep 3, 2024

  1. remove annotated vardict and tnscope intermediate files

    @mathiasbio
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  2. update docs and to tga tnscope filters

    @mathiasbio
    mathiasbio committed Sep 3, 2024
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  3. add filters to constants

    @mathiasbio
    mathiasbio committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. change final umi bamfile name

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Commits on Sep 9, 2024

  1. remove alt_f1r2 filter from tga

    @mathiasbio
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  2. update docs

    @mathiasbio
    mathiasbio committed Sep 9, 2024
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  3. pon consent doc added

    @mathiasbio
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Commits on Sep 10, 2024

  1. Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BAL… 

    …SAMIC into update_cnvkit_pons
    @mathiasbio
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  2. Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

    @mathiasbio
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Commits on Sep 11, 2024

  1. add trim soft clip to tnscope tga

    @mathiasbio
    mathiasbio committed Sep 11, 2024
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  2. revert sentieon alignmetrics to picard due to missing values

    @mathiasbio
    mathiasbio committed Sep 11, 2024
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  3. bug fix

    @mathiasbio
    mathiasbio committed Sep 11, 2024
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Commits on Sep 16, 2024

  1. add genmod to all workflows

    @mathiasbio
    mathiasbio committed Sep 16, 2024
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  2. bug fix

    @mathiasbio
    mathiasbio committed Sep 16, 2024
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  3. fix bug

    @mathiasbio
    mathiasbio committed Sep 16, 2024
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  4. fix

    @mathiasbio
    mathiasbio committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. add ranked files to delivery

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  2. fix bug for wgs flow

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  3. fix

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  4. add vardict raw to delivery rule

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  5. add DP and AF to info field of TNscope

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  6. fix

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  7. black

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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  8. fix

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    mathiasbio committed Sep 17, 2024
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  9. fix

    @mathiasbio
    mathiasbio committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. add modify tnscope to umi flow

    @mathiasbio
    mathiasbio committed Sep 18, 2024
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  2. fix bugs

    @mathiasbio
    mathiasbio committed Sep 18, 2024
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  3. change file delivery tags

    @mathiasbio
    mathiasbio committed Sep 18, 2024
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  4. return tag to research

    @mathiasbio
    mathiasbio committed Sep 18, 2024
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  5. fix delivery

    @mathiasbio
    mathiasbio committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. add tumor vep

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  3. test

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  4. store unfiltred research annotated snvs

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  5. rename ranked to scored

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  6. bug fix

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  7. fix umi cram

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  8. bug fix

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  9. if statement for normal

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  10. del

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  11. fix tag

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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  12. rename tag

    @mathiasbio
    mathiasbio committed Sep 19, 2024
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Commits on Sep 20, 2024

  1. bug fix

    @mathiasbio
    mathiasbio committed Sep 20, 2024
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Commits on Sep 23, 2024

  1. Merge branch 'cnvkit_to_gens' into merge_vardict_tnscope

    @mathiasbio
    mathiasbio authored Sep 23, 2024
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Commits on Oct 1, 2024

  1. add found in to vcfs

    @mathiasbio
    mathiasbio committed Oct 1, 2024
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  2. Merge branch 'merge_vardict_tnscope' of github.com:Clinical-Genomics/… 

    …BALSAMIC into merge_vardict_tnscope
    @mathiasbio
    mathiasbio committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. add rankscore familyid

    @mathiasbio
    mathiasbio committed Oct 2, 2024
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Commits on Oct 9, 2024

  1. switch orders of tnscope and vardict for merging

    @mathiasbio
    mathiasbio committed Oct 9, 2024
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  2. bug fix

    @mathiasbio
    mathiasbio committed Oct 9, 2024
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Commits on Oct 11, 2024

  1. add back tiddit

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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  2. fix conflicts

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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  3. black

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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  4. fix

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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  5. fix umi

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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  6. remove accidentally added testfile

    @mathiasbio
    mathiasbio committed Oct 11, 2024
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Commits on Oct 14, 2024

  1. remove research filtered pass from deliver

    @mathiasbio
    mathiasbio committed Oct 14, 2024
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  2. update docs

    @mathiasbio
    mathiasbio committed Oct 14, 2024
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  3. changelog

    @mathiasbio
    mathiasbio committed Oct 14, 2024
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