v12.1.0

GENIE releases:

• 9.5-consortium

Changelog:

• Reorganize directory structures
• Update logging
• Remove unused scripts

v12.0.0

GENIE releases:

• 9.4-consortium

Changelog:

• Split GENIE file format registry from GENIE package
• Added create-case-lists cli
• use assay information to create case list files instead of gene matrix file
• Improve clinical attribute mapping during input to database step
• Support pandas>=1.1
• Added create new database functions
• Added get-invalid-errors cli function

v11.1.0

GENIE releases:

9.3-consortium

Changelog:

• lock pandas==1.0 because pandas>1 not compatible with code yet
• fix data guide to use SEQ_PIPELINE_ID instead of SEQ_ASSAY_ID
• add provenance to use version of code executed for release files
• add TSA1 and TSA2 validation for maf files

v11.0.0

GENIE releases:

9.1-consortium, 9.2-consortium

Changelog:

• Update Docker environment
• Use genome nexus instead of vcf2maf for annotation
• Fix mafinbed filter issue

What's Changed

• v11 - 9.X release series by @thomasyu888 in #331
• Fix by @thomasyu888 in #335
• VCF sometimes has non-ascii characters so break right after headers by @thomasyu888 in #338
• Fix XML install by @thomasyu888 in #341
• Dont use old germline filter by @thomasyu888 in #342
• Fix maf in bed filter by @thomasyu888 in #344

Full Changelog: v10.0.0...v11.0.0

v10.0.0

GENIE releases:

• 8.5-consortium
• 8.0-public

Changelog:

• synapseclient<2 not supported
• use unittest.mock instead of mock
• Separate consortium_to_public cli from genie module

What's Changed

• Move get center files outside of validation function by @thomasyu888 in #289
• Separate building of validation and error dataframe by @thomasyu888 in #288
• Remove test parameter from input_to_database by @thomasyu888 in #253
• Update database mapping synapse id so that correct table is updated by @thomasyu888 in #299
• Fix MAF validation by @thomasyu888 in #297
• v10.0.0 by @thomasyu888 in #303
• Fix duplicated error tracking by @thomasyu888 in #309
• frequently mutated genes dashboard table should only show non-synonymous variants by @thomasyu888 in #313
• Push dev by @thomasyu888 in #312
• Use ghaction test by @thomasyu888 in #314
• Release to pypi by @thomasyu888 in #275
• Re organize consortium_to_public.py by @thomasyu888 in #131
• Bundle appropriate SEQ_ASSAY_IDs with their SEQ_PIPELINE_ID by @thomasyu888 in #301
• Add test for removeStringFloat() by @karawoo in #325
• Use unittest.mock instead of mock by @thomasyu888 in #317
• Remove synapseclient < 2 support by @thomasyu888 in #318
• Fix merge cna function by @thomasyu888 in #328
• Consortium to public by @thomasyu888 in #329
• v10 by @thomasyu888 in #326

New Contributors

• @karawoo made their first contribution in #325

Full Changelog: v9.0.0...v10.0.0

v9.0.0

GENIE releases:

• 8.4-consortium

Changelog:

• pd.np and pd.utils is deprecated in the future
• Fixed duplicated error email
• Fixed filetype parameter
• Improve dashboard
• support Texlive for data guide generation
• Update to synapseclient==2.0
• Format SEQ_PIPELINE_ID

v8.0.0

GENIE releases:

• 8.3-consortium

Changelog:

• Automate data guide (known bug with not having all the dependencies in Dockerfile)
• Add SEQ_PIPELINE_ID to assay information Table
• Redact clinical values prior to storing into Synapse Tables
• If there are no valid clinical files don't process

What's Changed

• Add in seq pipeline id by @thomasyu888 in #264
• Begin auto generation of data guide by @thomasyu888 in #255
• Refactor Redaction Policy by @thomasyu888 in #270
• v8.0.0 by @thomasyu888 in #273
• Make sure if there are no valid clinical files that nothing is appended by @thomasyu888 in #279

Full Changelog: v7.0.1...v8.0.0

v7.0.1

• Add in missed support synapseclient v2.0.0

v7.0.0

Changelog:

• Change specimen_type to preservation_technique
• pin down synapseclient version
• no PHI in clinical database
• python 3.6+ support
• add support for synapseclient 2.0 but will soon deprecate use of synapseclient < 2

What's Changed

• Change specimen_type -> preservation_technique by @thomasyu888 in #256
• Database can't have PHI by @thomasyu888 in #249
• Prepare syn client 2.0 by @thomasyu888 in #254
• v7.0.0 release by @thomasyu888 in #263

Full Changelog: v6.0.0...v7.0.0

v6.0.0

GENIE releases:

• 8.2-consortium

Changelog:

• Updated dashboard

What's Changed

• DEV: remove unusable dashboard plots by @thomasyu888 in #233
• Add version to genie cli by @thomasyu888 in #251
• Add in gene panel and bed differences by @thomasyu888 in #247
• Remove validation of values for target_capture_kit by @thomasyu888 in #250
• set to_validate outside of for loop so it doesn't get reset by @thomasyu888 in #248
• v6.0.0 release by @thomasyu888 in #252
• Fix dashboard by @thomasyu888 in #259

Full Changelog: v5.0.0...v6.0.0