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feat: test v17 snv changes#1513

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mathiasbio wants to merge 60 commits intomasterClinical-Genomics/BALSAMIC:masterfrom test_v17_snv_changesClinical-Genomics/BALSAMIC:test_v17_snv_changesCopy head branch name to clipboard

+1,096-191

Commits

Commits on Nov 11, 2024

• add merge script

  mathiasbio

  committed
  de62484

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• replace bcftools with custom script

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  committed
  1605c8c

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• fix script

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  committed
  35401bc

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Commits on Nov 12, 2024

• update vcfpy

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  committed
  c99b1e6

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• black

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  a34f0fc

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• add more docstrings and typehints

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  committed
  b3d5271

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• fix

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  committed
  29e87a6

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• add RPA filter

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  committed
  be9373d

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• add rpa filter to tumor only

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  committed
  3cd7cdc

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• add rpa to params

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  committed
  4bda98f

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• set maximum rpa to 10

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  committed
  61069d4

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• attempt fix

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  committed
  bee17f0

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Commits on Nov 20, 2024

• update script

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  committed
  870820b

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Commits on Nov 21, 2024

• fixes

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  committed
  0bf6a27

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• fix

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  committed
  c5da949

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• fix

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  committed
  f93d44e

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

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  committed
  92afcd0

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• Merge branch 'master' into develop

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  committed
  67c6701

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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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  committed
  cd6ee22

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• reformat

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  committed
  2a3dd7d

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Commits on Nov 28, 2024

• try

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  committed
  95c06ef

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Commits on Nov 29, 2024

• fix

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  committed
  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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  committed
  ea4b5ce

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• black

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  committed
  f60adac

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• changelog

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  committed
  3874a90

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• fix

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  committed
  6b3fe6e

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• fix

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  committed
  e96a980

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Commits on Dec 10, 2024

• new filter

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  committed
  68aeae1

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• convert to list

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  committed
  24fd9a1

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Commits on Dec 16, 2024

• major refactor of filter logic

  mathiasbio

  committed
  13fab22

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• bug fixes

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  committed
  c66a66e

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• fix

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  committed
  72cfbe1

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• fix

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  committed
  50fbc0a

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• test

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  committed
  61aa1ab

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• fix

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  committed
  28de8d4

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• fix bug

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  committed
  f3f5cb2

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Commits on Dec 17, 2024

• fix

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  committed
  3095fd9

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• black

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  committed
  b2c62c6

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• update comments

  mathiasbio

  committed
  d435039

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• fix clinical and research filters

  mathiasbio

  committed
  eb46385

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• Merge branch 'merge_snv_variants_script' into test_v17_snv_changes

  mathiasbio

  committed
  4ed6303

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• Merge branch 'disable_normal_hardfilter' into test_v17_snv_changes

  mathiasbio

  committed
  82b8f62

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• merge softfilter

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  committed
  6d77bf3

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• Merge branch 'add_rpa_filter' into test_v17_snv_changes

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  committed
  f657e63

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Commits on Dec 18, 2024

• fix vardict tn hardfilters

  mathiasbio

  committed
  7c3a484

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

  mathiasbio

  committed
  a3b89fb

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• Merge branch 'disable_normal_hardfilter' into test_v17_snv_changes

  mathiasbio

  committed
  f9d96f9

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• update vardict hardfilters

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  committed
  0456b05

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

  mathiasbio

  committed
  a97760b

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• Merge branch 'disable_normal_hardfilter' into test_v17_snv_changes

  mathiasbio

  committed
  c3b2b5f

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• remove pass and triallelic site prefilters

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  committed
  f29b271

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

  mathiasbio

  committed
  f47e9e8

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• Merge branch 'disable_normal_hardfilter' into test_v17_snv_changes

  mathiasbio

  committed
  2aceb11

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• fix bug

  mathiasbio

  committed
  84dd929

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

  mathiasbio

  committed
  169ef1a

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• Merge branch 'disable_normal_hardfilter' into test_v17_snv_changes

  mathiasbio

  committed
  9af4d7e

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