v5.0.0

GENIE releases:

• 8.1-consortium

Changelog:

• Updated dashboard with top mutations TP53 flag
• Pass in list of entities for validation
• Filter out common variants from consortium release

What's Changed

• Pass in entity list into genie validator to obtain filetype by @thomasyu888 in #235
• Remove germline variants by @thomasyu888 in #236
• Make sure not having optional columns doesn't fail validation by @thomasyu888 in #238
• SAGE shouldn't be the default center by @thomasyu888 in #239
• CHROM, POS in vcf can't be null by @thomasyu888 in #240
• Pass along entity name by @thomasyu888 in #243
• Update dashboards by @thomasyu888 in #237
• Fix ethnicity race dashboard by @thomasyu888 in #246
• Since the file is no longer renamed after download, must pass in entity name by @thomasyu888 in #244

Full Changelog: v4.0.0...v5.0.0

v4.0.0

Big refactor to begin true semantic versioning. Prior to this, releasees of software were tied to GENIE data releases. This shouldn't be the case. There will be releases tied to versions of the software, but the software should be continuously worked on.

What's Changed

• separate input to db main into a script by @kdaily in #113
• remove out of date comment by @kdaily in #118
• Refactor input_to_db -> _get_status_and_error_list by @thomasyu888 in #120
• Refactor input_to_db -> validate.py by @thomasyu888 in #126
• Refactor input_to_db -> Abstraction of getting duplication error by @thomasyu888 in #138
• Python3 by @kdaily in #144
• do not use the syn object by @kdaily in #146
• Use entity objects by @kdaily in #145
• abstract modified on to a function by @kdaily in #150
• remove dependency on input_to_database by @kdaily in #156
• use argparser to manage exclusive options by @kdaily in #155
• Generalize shared functions by @kdaily in #157
• Refactor validate command line by @kdaily in #159
• do not run bed test if no bedtools found. by @kdaily in #161
• get rid of try/catch to find one specific error. by @kdaily in #160
• Clinical use preprocess / get_dataframe by @thomasyu888 in #151
• DEV: Add unit tests for processfiles by @thomasyu888 in #153
• input_to_database: Pass in oncotree link by @thomasyu888 in #158
• DEV: Restrict genie package to use python 3 by @thomasyu888 in #102
• DEV: Refactor input_to_database.py by @thomasyu888 in #60
• Remove self import. by @kdaily in #177
• No syn for get status and error by @kdaily in #180
• DEV: Fix logging of GENIE by @thomasyu888 in #175
• Make validate class by @kdaily in #176
• Move tests out of unit folder by @thomasyu888 in #184
• Format registry using introspection from base class by @kdaily in #186
• Abstract validate single file and standardize testing setup by @kdaily in #187
• Standardize oncotree and nosymbolcheck parameters by @kdaily in #188
• Quick fixes by @thomasyu888 in #191
• DEV: Refactor database_to_staging.py by @thomasyu888 in #88
• add package version by @kdaily in #193
• store fileType in validation status table. by @kdaily in #198
• Format registry as list by @kdaily in #195
• add filetype to error table and fix tests. by @kdaily in #199
• Lint bed file by @thomasyu888 in #202
• Standardize adding of filetype and center to validation and error status lists by @thomasyu888 in #200
• Create gene panel should happen outside of the bed class by @thomasyu888 in #203
• Add db to staging script to setup by @thomasyu888 in #194
• DEV: Refactor bed class by @thomasyu888 in #172
• Revert lint by @thomasyu888 in #206
• DEV: Update ubuntu version and dependencies by @thomasyu888 in #164
• Lint assay by @thomasyu888 in #210
• use temp file to update database by @kdaily in #212
• send digest emails for notifications by @kdaily in #213
• Fix processing errors by @thomasyu888 in #214
• Update setup.py by @kdaily in #216
• simplify validating single file return by @kdaily in #223
• remove all references to threads. by @kdaily in #221
• remove gzip dependency, seems unused by @kdaily in #224
• DEV: Add in more yaml fields by @thomasyu888 in #170
• DEV: Specify versions of packages in Dockerfile by @thomasyu888 in #231
• DEV: Don't do mafinbed filter for centers not being processed by @thomasyu888 in #227
• DEV: cases_sequenced wasn't containing WES samples by @thomasyu888 in #228
• DEV: No duplicated variants in vcf / maf by @thomasyu888 in #229
• DEV: assay information release file by @thomasyu888 in #232
• Develop -> Master by @thomasyu888 in #226
• Push version by @thomasyu888 in #234

Full Changelog: v3.4...v4.0.0

v3.4

GENIE releases:

• 7.5-consortium

Changelog:

• Don't check symbols for fusion files

v3.3

GENIE releases:

• 7.4-consortium

Changelog:

• Change bed file name to genomic_information.txt
• Update Dockerfile

v3.2

GENIE releases:

• 7.2-consortium

Changelog:

• Exclude WES panels from gene panel / gene matrix
• Allow numerical sample and patient names
• Add in variant counts

v3.1

GENIE releases:

• 7.1-consortium

Changelog:

• Add in vital status to release

v3.0

GENIE releases:

• 6.6-consortium
• 6.0-public

Changelog:

• Remove maf header as included in case_list files

v2.5

GENIE releases:

• 6.5-consortium

Changelog:

• Fix mutation in cis filter

v2.4

GENIE releases:

• 6.4-consortium

Changelog:

• Add case_list_all file
• Fix yaml.load deprecation

What's Changed

• Fix yaml load deprecation by @thomasyu888 in #78
• Move vcf2maf dockerfile to home directory by @thomasyu888 in #79
• create _all caselist by @thomasyu888 in #86

Full Changelog: v2.3...v2.4

v2.3

GENIE releases:

• 6.3-consortium

Changelog:

• Add blacklist variants
• Samples part of SEQ_ASSAY_ID with no bed files are filtered out

What's Changed

• Add in assay information by @thomasyu888 in #67
• pass in genie user and genie pass to dashboard markdown gen by @thomasyu888 in #74
• Add in no gene panel filter by @thomasyu888 in #77
• Add blacklist variants to dashboard markdown by @thomasyu888 in #76

Full Changelog: v2.2.1...v2.3