Sage-Bionetworks/Genie

Issues

• MAF file validation

  #512 opened 2 years ago by jakevc
  1

• updated required pandas version to be >=1.3.5

  #467 opened 2 years ago by thomasyu888
  0

• Keyring version not compatible with python 3.10

  #412 opened 2 years ago by jakevc
  2

• Update SEQ_DATE error message

  #465 opened 2 years ago by thomasyu888
  0

• Check CONTACT <= death dates

  #466 opened 2 years ago by thomasyu888
  0

• Cross file validation

  #409 opened 2 years ago by thomasyu888
  0

• Deal with non-ascii characters

  #343 opened 2 years ago by thomasyu888
  1

• Make sure fusion Entrez_Gene_Id column is integer or float

  #390 opened 2 years ago by thomasyu888
  0

• DOD shouldn't be before other Dates

  #336 opened 2 years ago by thomasyu888
  0

• Add validation check for SAMPLE_ID

  #443 opened 2 years ago by hhunterzinck
  1

• Add clinicalReported to genomic information file

  #458 opened 2 years ago by thomasyu888
  0

• Modify vital status inconsistency check

  #463 opened 2 years ago by hhunterzinck
  0

• Create Release 13.1.1

  #451 opened 3 years ago by thomasyu888
  0

• Modify check for DEAD variable in clinical file

  #449 opened 3 years ago by hhunterzinck
  0

• Docker build not working

  #442 opened 3 years ago by thomasyu888
  0

• Add SAMPLE_CLASS filter to remove cfDNA samples for public release

  #410 opened 3 years ago by thomasyu888
  0

• Fix the GENIE install for the docker image

  #432 opened 3 years ago by thomasyu888
  0

• Modify error message for maf.py check

  #434 opened 3 years ago by hhunterzinck
  0

• Make validation of SEQ_ASSAY_IDs case-insensitive

  #435 opened 3 years ago by hhunterzinck
  1

• Validation of clinical files fails with numpy error

  #426 opened 3 years ago by jakevc
  1

• Document new GENIE code SOP

  #368 opened 3 years ago by thomasyu888
  0

• Validation of missing SEQ_ASSAY_ID in assay_information.yaml file

  #402 opened 3 years ago by thomasyu888
  0

• Add tests for retry_get_url

  #322 opened 3 years ago by karawoo
  1

• Add tests for store_file

  #321 opened 3 years ago by karawoo
  1

• Add test for find_caselistid

  #320 opened 3 years ago by karawoo
  1

• Fix dockerfile

  #393 opened 4 years ago by thomasyu888
  0

• t_depth, t_alt_count, t_ref_count calculation and validation

  #376 opened 4 years ago by thomasyu888
  3

• Release v12.3.0

  #381 opened 4 years ago by thomasyu888
  0

• Create new variant filter: Remove blacklist variants / possible artifacts

  #383 opened 4 years ago by thomasyu888
  1

• Make consortium releases the same as public release

  #382 opened 4 years ago by thomasyu888
  0

• Public data guide should not have vital status columns

  #333 opened 4 years ago by thomasyu888
  0

• Must query all file views twice to make sure the newest version is received.

  #340 opened 4 years ago by thomasyu888
  1

• Strip white space from Reference_Allele and TSA2.

  #377 opened 4 years ago by thomasyu888
  0

• CHOP sample has duplicated variant

  #378 opened 4 years ago by thomasyu888
  0

• Release 12.2.0

  #369 opened 4 years ago by thomasyu888
  0

• Fusion file can't have any blank Hugo_Symbol

  #370 opened 4 years ago by thomasyu888
  0

• Add provenance

  #356 opened 4 years ago by thomasyu888
  1

• Release 12

  #361 opened 4 years ago by thomasyu888
  0

• Create breakdown of the SEQ_DATE distribution per site

  #339 opened 4 years ago by thomasyu888
  1

• Pandas v1.1 fails clinical tests

  #345 opened 4 years ago by thomasyu888
  1

• Update aacrgenie to synapsegenie

  #307 opened 4 years ago by thomasyu888
  1

• Fix test coverage

  #315 opened 4 years ago by thomasyu888
  1

• Move AACR GENIE specific code into its own repo

  #330 opened 4 years ago by thomasyu888
  0

• Edit error message for YEAR validation

  #337 opened 4 years ago by thomasyu888
  0

• Add other SAMPLE_TYPE to data guide in clinical

  #332 opened 4 years ago by thomasyu888
  0

• Remove support for synapseclient<2

  #311 opened 4 years ago by thomasyu888
  0

• Add tests for removeStringFloat

  #323 opened 4 years ago by karawoo
  1

• use unittest.mock instead of mock

  #316 opened 4 years ago by thomasyu888
  0

• Adjust frequently mutated genes to only have non-synonymous variants

  #310 opened 4 years ago by thomasyu888
  0

• Fix invalid error not being stored

  #308 opened 4 years ago by thomasyu888
  0