Code

feat: add tga cnvkit to gens#1448

Code

Merged

mathiasbio merged 65 commits intoupdate_cnvkit_ponsClinical-Genomics/BALSAMIC:update_cnvkit_ponsfrom cnvkit_to_gensClinical-Genomics/BALSAMIC:cnvkit_to_gensCopy head branch name to clipboardOct 11, 2024

+635-200

Commits

Commits on Jun 14, 2024

• add gens functionality to tga

  mathiasbio

  committed
  e6516d6

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• add gens inputs

  mathiasbio

  committed
  7f6e521

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• add gens gnomad af to tga

  mathiasbio

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  24e41a9

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• black

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  cdbe43f

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• fix

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  f262919

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• fix

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  c2aafb9

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Commits on Jun 17, 2024

• fix

  mathiasbio

  committed
  cc9e506

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• fix

  mathiasbio

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  d471395

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• fix

  mathiasbio

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  05bd3ae

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• doc strings and named args

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  6868556

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• black

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  b03a9f0

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• changelog

  mathiasbio

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  582cfb0

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• bug fix

  mathiasbio

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  e9c4c7f

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• fix

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  8f88da7

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• lower padding

  mathiasbio

  committed
  4a4671e

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Commits on Jun 18, 2024

• add tumor purity adjustment to gens cov file

  mathiasbio

  committed
  5bcf768

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Commits on Jun 19, 2024

• typehints

  mathiasbio

  committed
  acde38f

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• black

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  ed4c018

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• fix pytests

  mathiasbio

  committed
  a108a0e

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Commits on Jun 28, 2024

• update purity adjustment formula

  mathiasbio

  committed
  99d3d57

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• Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into develop

  mathiasbio

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  bf57f92

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• merge develop

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  d69c3c7

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• m conflict

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  44f25e1

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• m conflict

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  9335478

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Commits on Jul 15, 2024

• adjust formula

  mathiasbio

  committed
  5768116

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• add round

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  committed
  6433887

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Commits on Jul 23, 2024

• code review

  mathiasbio

  committed
  f3a2c66

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• fix merge conflicts

  mathiasbio

  committed
  2de2692

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Commits on Jul 24, 2024

• fix bug

  mathiasbio

  committed
  2b91865

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• float

  mathiasbio

  committed
  821bbd3

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• comment out purity and ploidy adjustment

  mathiasbio

  committed
  6aa5510

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Commits on Jul 25, 2024

• adjust purity and ploidy

  mathiasbio

  committed
  f703189

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• bug fix

  mathiasbio

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  8994fc8

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• remove purity and ploidy adjustment

  mathiasbio

  committed
  11be7bf

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Commits on Jul 29, 2024

• new threads

  mathiasbio

  committed
  3d44b03

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Commits on Jul 31, 2024

• return purity adjustment

  mathiasbio

  committed
  b484670

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• code review

  mathiasbio

  committed
  1fac876

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Commits on Aug 1, 2024

• new purity and ploidy formula from PureCN

  mathiasbio

  committed
  9688e3d

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Commits on Aug 2, 2024

• merge pon repo

  mathiasbio

  committed
  8d80a75

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• fix pytests

  mathiasbio

  committed
  3abae1b

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• black

  mathiasbio

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  ce95786

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Commits on Aug 8, 2024

• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  d736f7c

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  4f7cf28

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Commits on Aug 9, 2024

• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  8f32eac

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  ca32fea

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• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  0c99f60

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  f5eebd6

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• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  8a40907

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  254c6a8

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• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  42c314a

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  e3f54f7

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Commits on Aug 13, 2024

• add io test

  mathiasbio

  committed
  6030b87

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• add new test

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Commits on Aug 15, 2024

• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  92b5c4d

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  2a07bb1

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Commits on Sep 10, 2024

• Merge branch 'update_cnvkit_pons' of github.com:Clinical-Genomics/BALSAMIC into update_cnvkit_pons

  mathiasbio

  committed
  3f6b529

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• Merge branch 'update_cnvkit_pons' into cnvkit_to_gens

  mathiasbio

  committed
  9569ebd

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Commits on Oct 10, 2024

• remove purity adjustment

  mathiasbio

  committed
  b86d6f4

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• black

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  139c11e

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• add pytest

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  7e567fd

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• black

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  ce98baa

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• clean up

  mathiasbio

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  cf739dc

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• clean up

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  7138553

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• return tiddit

  mathiasbio

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  1e230bb

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• fix code smells

  mathiasbio

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  a420abb

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