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fix: merge snv variants script#1499

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mathiasbio wants to merge 167 commits intodevelopClinical-Genomics/BALSAMIC:developfrom merge_snv_variants_scriptClinical-Genomics/BALSAMIC:merge_snv_variants_scriptCopy head branch name to clipboard

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Commits on Nov 11, 2024

• add merge script

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  de62484

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• replace bcftools with custom script

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  1605c8c

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• fix script

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  35401bc

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Commits on Nov 12, 2024

• update vcfpy

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  c99b1e6

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• black

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  a34f0fc

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• add more docstrings and typehints

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  b3d5271

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• fix

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  29e87a6

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• add RPA filter

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  be9373d

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• attempt fix

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  bee17f0

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Commits on Nov 20, 2024

• update script

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  870820b

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Commits on Nov 21, 2024

• fixes

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  0bf6a27

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• fix

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  c5da949

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• fix

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  f93d44e

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• Merge branch 'develop' into merge_snv_variants_script

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  bfdd6e1

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

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  5b9d7c7

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• black

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  2fab1f3

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• revert

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  cd6ee22

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• reformat

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  2a3dd7d

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Commits on Nov 28, 2024

• try

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  95c06ef

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Commits on Nov 29, 2024

• fix

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  66e642c

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

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  committed
  0862377

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• rework bcftools filter

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• black

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  f60adac

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• changelog

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  3874a90

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• fix

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  6b3fe6e

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• fix

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  e96a980

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Commits on Dec 10, 2024

• new filter

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  68aeae1

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• convert to list

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  24fd9a1

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Commits on Dec 16, 2024

• major refactor of filter logic

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  committed
  13fab22

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• bug fixes

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  c66a66e

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• fix

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• fix

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• test

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  61aa1ab

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• fix

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  28de8d4

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• fix bug

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  f3f5cb2

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Commits on Dec 17, 2024

• fix

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  3095fd9

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• black

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  b2c62c6

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• update comments

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  d435039

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• fix clinical and research filters

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  eb46385

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Commits on Dec 18, 2024

• fix vardict tn hardfilters

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  committed
  7c3a484

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• update vardict hardfilters

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  0456b05

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• remove pass and triallelic site prefilters

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  f29b271

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• fix bug

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  committed
  84dd929

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Commits on Jan 15, 2025

• update script

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  committed
  a4844b6

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Commits on Jan 17, 2025

• add sentieon script

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  committed
  f63a41a

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Commits on Jan 20, 2025

• clean up found in, and adding custom section to header

  mathiasbio

  committed
  568e5dd

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• update

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  94a4503

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• add new rule

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• add license

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• format black sentieon script

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  9d30b8f

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• test

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  7efbf41

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Commits on Jan 21, 2025

• update

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  committed
  7698e73

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• change script

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  8469b0d

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• fix

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  3b8aede

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• fix

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• return MERGED filter

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  committed
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• test

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  55edd9b

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• fix

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• test

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  14c134d

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• fix

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• fix

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• test

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• test

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  54dd105

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• fix

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  1e7d7ce

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• set merged

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  2372e2d

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• fix

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• refactor

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• test

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  5d76ac0

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• fix

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• fix typehints

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• black etc

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• refactor

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• black

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  d407e63

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• change script

  mathiasbio

  committed
  5dc899b

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• change raw delivery vcf file for UMI and standard tga

  mathiasbio

  committed
  654e996

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• changelog

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  committed
  805ff7e

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• refactor

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  committed
  8056694

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Commits on Jan 23, 2025

• start refactor

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  ab8cc0e

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Commits on Jan 24, 2025

• refactor continues

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  98fcee4

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• propogate refactor to rules

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  committed
  72ab2dc

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• fix model

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  committed
  a5b0247

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• bug fix

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  committed
  25e97c7

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• clean up old code

  mathiasbio

  committed
  b30b667

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• refactor constant

  mathiasbio

  committed
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• add BioinfoTools constant to balsamic smk

  mathiasbio

  committed
  15a9d1a

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• remove umi param from general tga

  mathiasbio

  committed
  229e763

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• removing unussed analysis workflow param

  mathiasbio

  committed
  2c64e95

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• refactor

  mathiasbio

  committed
  7edc4d6

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

  mathiasbio

  committed
  8975592

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• merge develop

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  committed
  930d0ad

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• fix

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  committed
  b6632a9

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• fix

  mathiasbio

  committed
  8636569

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Commits on Jan 27, 2025

• fix clinical hard filters

  mathiasbio

  committed
  39fcb05

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• fix soft filter

  mathiasbio

  committed
  c778a16

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• refactor

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  committed
  8164e8e

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• refactor names

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  committed
  aff2b8c

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• fix pytest

  mathiasbio

  committed
  6b5c1ce

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• add new filter

  mathiasbio

  committed
  2c4cc23

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• add pytests

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  committed
  c7b301e

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• update test names

  mathiasbio

  committed
  a598574

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• remove unused function

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  committed
  ff86e7d

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• black

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  committed
  4cc420e

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Commits on Jan 28, 2025

• add new vardict filter

  mathiasbio

  committed
  c47fbd2

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• corrected vardict strandbias to be general

  mathiasbio

  committed
  dff2a39

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• add filter and mark it will be ignored

  mathiasbio

  committed
  d66e4a2

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• remove filters that will be removed

  mathiasbio

  committed
  2d66075

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• updated docs

  mathiasbio

  committed
  85b2a20

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• fix pytest

  mathiasbio

  committed
  8490657

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Commits on Jan 29, 2025

• change logic of mnv filters

  mathiasbio

  committed
  7e49b70

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

  mathiasbio

  committed
  01fae23

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• merge with softfilter branch

  mathiasbio

  committed
  a2390ae

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• fix filters

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  committed
  44b11e9

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• unpack set

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  committed
  064a7b1

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• rename filter

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  committed
  b17c384

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• change order of mnv processing

  mathiasbio

  committed
  8f0d7a2

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• fix bug

  mathiasbio

  committed
  8dcc3c5

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• fix bug

  mathiasbio

  committed
  ac6fe6f

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Commits on Jan 30, 2025

• add hard filter of MERGED variants

  mathiasbio

  committed
  d2de191

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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

  mathiasbio

  committed
  2dd995a

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• merge with other PRs

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• black

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  d9b2ff7

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• add to docs

  mathiasbio

  committed
  c15c8c9

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

  mathiasbio

  committed
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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

  mathiasbio

  committed
  4ca7fd6

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• fix filter

  mathiasbio

  committed
  b743d4d

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

  mathiasbio

  committed
  dd4b299

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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

  mathiasbio

  committed
  83f02a3

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Commits on Jan 31, 2025

• convert filter to infofield

  mathiasbio

  committed
  1282707

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• bug fix

  mathiasbio

  committed
  6dbc9a3

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• clean up

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  committed
  32844de

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• try to fix

  mathiasbio

  committed
  04bf774

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• testing

  mathiasbio

  committed
  40895fd

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• change filter

  mathiasbio

  committed
  c05036b

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

  mathiasbio

  committed
  d5de252

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• merge develop

  mathiasbio

  committed
  ed2ea13

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Commits on Feb 3, 2025

• fix

  mathiasbio

  committed
  e5c6e2e

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

  mathiasbio

  committed
  546bb46

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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

  mathiasbio

  committed
  38c6ebd

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• add pytests

  mathiasbio

  committed
  a89cecc

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• correct assert

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• add new assert

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• black

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  5cc8c2d

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Commits on Feb 4, 2025

• fix

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  6a72ac2

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• refactor code

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• black

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  36b7eb6

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• refactor

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• rename

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  3b1a9a1

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• correct pytest

  mathiasbio

  committed
  4f97933

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

  mathiasbio

  committed
  e3b0efe

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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

  mathiasbio

  committed
  e934b85

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Commits on Feb 5, 2025

• refactor

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  3c85260

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• fix

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  8f628cb

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• fix

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• fix

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• fix tumor and normal af

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• fix

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  520b08a

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• fix

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• update docs

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• remove file

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• remove file

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• black

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  76fcfbb

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

  mathiasbio

  committed
  04d51fd

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• merge develop

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  committed
  b73d372

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• refactor names

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  ca88e5e

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• fix

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  committed
  02c1a28

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Commits on Feb 6, 2025

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

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• Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script

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