v3.4.2

Changes

• Revert "Add work around for tokens time out" @jfkonecn (#237)
• Add work around for tokens time out @jfkonecn (#234)
• Typo in mutationtypeconsequencemap ? @n1zea144 (#227)
• Change scripts to pull python version from the env, executable from path @nodrogluap (#222)

🐛 Bug Fixes

• Set functional fusion to false when annotating intragenic SV @calvinlu3 (#231)
• Fix/git actions @calvinlu3 (#229)

📘 Documentation

• Update readme on vcf2maf @calvinlu3 (#230)

🕵️‍♀️ Full commit logs

• v3.4.1...v3.4.2

v3.4.1

🐛 Bug Fixes

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

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• v3.2.3...v3.2.4

v3.2.3

🧬 Features

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

🕵️‍♀️ Full commit logs

• 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)

🕵️‍♀️ Full commit logs

• v3.2.1...v3.2.2

v3.2.1

🐛 Bug Fixes

• Fix citation columns misalignment @zhx828 (#144)

🕵️‍♀️ Full commit logs

• v3.2.0...v3.2.1