v3.4.1

🐛 Bug Fixes

• Support Tumor_Sample_Barcode as column name in clinical file @zhx828 (#215)

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• v3.4.0...v3.4.1

v3.4.0

🧬 Features

• Add option to include descriptions & Add additional columns when annotating genomic change @zhx828 (#204 #210)
• Add additional columns when annotating genomic change @zhx828 (#208)

🧰 Maintenance

• Bump requests from 2.27.1 to 2.31.0 in /requirements @dependabot (#200)

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• v3.3.2...v3.4.0

v3.3.2

Changes

• Updates to annotator by genomic change @zhx828 (#191)
  • Make TUMOR_SEQ_ALLELE1 column optional, it is usually the reference allele
  • Support chr prefix for chromosome

🧬 Features

• Support python 3.11 @zhx828 (#190)
• Skip token validation if the url is specified by user that different from the default @zhx828 (#189)

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• v3.3.1...v3.3.2

v3.3.1

Changes

• Support additional SV headers @zhx828 (#184)

🧰 Maintenance

• Add flake8 github action and fix all flake8 errors @zhx828 (#179)

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• v3.3.0...v3.3.1

v3.3.0

🧬 Features

• Support structural variant annotator (#161)
• Support individual CNA file format(#162)
• Validate oncokb token before starting the annotation (#163)
• Update logics on calculating highest TX level (#164)
• Add resistance mutations columns and split TX count column by sensitive and resistance (#173)
• Provide more info when required parameter of each annotator is missing(#174)

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• v3.2.4...v3.3.0

v3.2.4

Changes

• Update tests based on v3.12 @zhx828 (#165)

🐛 Bug Fixes

• Check whether level exists in the input file @zhx828 (#170)

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• v3.2.3...v3.2.4

v3.2.3

🧬 Features

• Add retry for annotation endpoints @zhx828 (#158)

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• v3.2.2...v3.2.3

v3.2.2

🐛 Bug Fixes

• make batches smaller and timeouts longer in Core @sheridancbio (#145)

👷‍♀️ Testing, Configuration & Deployment

• Upgrade release-drafter to 5.15.0 @zhx828 (#151)

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• v3.2.1...v3.2.2

v3.2.1

🐛 Bug Fixes

• Fix citation columns misalignment @zhx828 (#144)

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• v3.2.0...v3.2.1

v3.2.0

Changes

• Added a 2 minute timeout for all the requests @benglasstone (#138)

🧬 Features

• Split citations column to multiple based on data fields @zhx828 (#134)

🐛 Bug Fixes

• Strip column header to avoid unnecessary spaces @zhx828 (#140)
• Update bash scripts format following ShellCheck @zhx828 (#135)

👷‍♀️ Testing, Configuration & Deployment

• Update annotation tests to use the latest data @zhx828 (#142)

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• v3.1.1...v3.2.0