Ecosyste.ms: Issues

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GitHub / Sage-Bionetworks/Genie issues and pull requests

#580 - [GEN-1021] update library strategy

Pull Request - State: open - Opened by danlu1 19 days ago - 3 comments

#579 - [GEN-1545] Remove GERMLINE from valid values of the SV_STATUS

Pull Request - State: closed - Opened by danlu1 26 days ago - 1 comment

#578 - Update configure maf docstring

Pull Request - State: closed - Opened by rxu17 about 2 months ago - 1 comment

#577 - Update doctsrings of maf functions

Pull Request - State: closed - Opened by rxu17 4 months ago - 1 comment

#576 - [GEN-1429] Add variant_classification as known string col

Pull Request - State: closed - Opened by rxu17 4 months ago - 1 comment

#575 - Update docstring for cna's validateSymbol function

Pull Request - State: closed - Opened by rxu17 5 months ago - 1 comment

#574 - [GEN-703] Validation status with version

Pull Request - State: closed - Opened by thomasyu888 5 months ago - 3 comments

#572 - [GEN-1348] Allow in mapping tables

Pull Request - State: closed - Opened by rxu17 5 months ago - 1 comment

#571 - [GEN-1299] align col names

Pull Request - State: closed - Opened by thomasyu888 5 months ago - 2 comments

#570 - [GEN-1326] Remove panel overlap charts

Pull Request - State: closed - Opened by thomasyu888 5 months ago - 2 comments

#569 - [GEN-1325] Remove section on flagged mutations

Pull Request - State: closed - Opened by thomasyu888 5 months ago - 3 comments

#568 - [GEN-1330] Setup staging pipeline

Pull Request - State: closed - Opened by rxu17 6 months ago - 4 comments

#567 - [GEN-1313] Export detailed columns for NAACCR codes

Pull Request - State: closed - Opened by danlu1 6 months ago - 2 comments

#566 - [GEN-1109] Setup base mkdocs for genie

Pull Request - State: closed - Opened by rxu17 6 months ago - 4 comments

#565 - [GEN-1294] pin r-base version and upgrade to Node 20

Pull Request - State: closed - Opened by danlu1 7 months ago - 2 comments

#564 - [GEN-1285] Remove row based validation

Pull Request - State: closed - Opened by danlu1 7 months ago - 1 comment

#563 - [GEN-1285] Remove row-based validation error message

Pull Request - State: closed - Opened by danlu1 7 months ago - 1 comment

#562 - [GEN-1263] Fix bed file duplicates

Pull Request - State: closed - Opened by rxu17 7 months ago - 5 comments

#561 - [GEN-867] Add validation rule to check if INT_DOD >= INT_CONTACT

Pull Request - State: closed - Opened by danlu1 7 months ago - 1 comment

#560 - [GEN-868] add year death validation

Pull Request - State: closed - Opened by danlu1 7 months ago - 2 comments

#559 - [GEN-178] Update to pandas 2.0 and upgraded synapseclient

Pull Request - State: open - Opened by rxu17 7 months ago - 2 comments

#558 - [GEN-1000] Refactor and sort unmapped oncotree codes in validation message

Pull Request - State: closed - Opened by rxu17 7 months ago - 2 comments

#557 - [GEN-1237] Add documentation to maf allele validation

Pull Request - State: closed - Opened by rxu17 8 months ago - 1 comment

#556 - [GEN-1164] add workflow to build docker image and push it to ghcr

Pull Request - State: closed - Opened by danlu1 8 months ago - 1 comment

#555 - [GEN-997] update method to concatenate columns for dataframe

Pull Request - State: closed - Opened by danlu1 8 months ago - 2 comments

#554 - [GEN-996] convert the clinical template columns from a set to a list

Pull Request - State: closed - Opened by danlu1 8 months ago - 2 comments

#553 - [GEN-1067] add functionality to warn for identical ref and tsa2

Pull Request - State: closed - Opened by danlu1 9 months ago - 2 comments

#552 - [GEN-1191] Add file logging

Pull Request - State: closed - Opened by rxu17 9 months ago - 1 comment

#551 - [GEN-1163] Hotfix for annotation-tools

Pull Request - State: closed - Opened by rxu17 9 months ago - 1 comment

#550 - [GEN-1065] Use OIDC with pypi in genie package publishing

Pull Request - State: closed - Opened by rxu17 9 months ago - 2 comments

#549 - [GEN-974] Allow NaN, nan and NA strings for mutation data

Pull Request - State: closed - Opened by rxu17 10 months ago - 1 comment

#548 - [GEN-1076] Exclude genomic_location_explanation from release

Pull Request - State: closed - Opened by rxu17 10 months ago - 4 comments

#546 - [GEN-1028] Generate failed annotations report dashboard

Pull Request - State: closed - Opened by rxu17 11 months ago - 6 comments

#545 - [GEN-1027] Store failed annotations error report

Pull Request - State: closed - Opened by rxu17 11 months ago - 3 comments

#544 - [GEN-1026] Output annotation error report

Pull Request - State: closed - Opened by rxu17 11 months ago - 1 comment

#543 - [GEN-1018] Update __main__.py and validate.py

Pull Request - State: closed - Opened by Chelsea-Na 11 months ago - 1 comment

#542 - Update docs

Pull Request - State: closed - Opened by rxu17 12 months ago

#541 - [GEN-977] update annotation-tools version

Pull Request - State: closed - Opened by rxu17 12 months ago

#540 - [GEN-973] Fix bed file-clinical file cross-validation

Pull Request - State: closed - Opened by rxu17 about 1 year ago

#539 - [GEN-809] Validate allele columns

Pull Request - State: open - Opened by rxu17 about 1 year ago

#537 - [GEN-834] Disable data guide generation

Pull Request - State: closed - Opened by rxu17 about 1 year ago

#536 - [GEN-846] & [GEN-845] Ignore case and allow underscores in cross-validate

Pull Request - State: closed - Opened by rxu17 about 1 year ago

#535 - [GEN-851] Hotfix pin cbioportal repo version

Pull Request - State: closed - Opened by rxu17 about 1 year ago

#534 - [GEN-833] Remove support for python 3.7, pin synapseclient

Pull Request - State: closed - Opened by rxu17 about 1 year ago

#533 - [GEN-738] Add variant position validation for maf file

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#532 - [GEN-498] Remove fusion files from public release

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#531 - [GEN-498] Remove fusion files from public release

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#530 - [GEN-756] Fix maf validation

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#529 - [GEN-478] Fix BIRTH_YEAR redaction

Pull Request - State: open - Opened by thomasyu888 over 1 year ago - 1 comment

#528 - fix: update maf read_csv

Pull Request - State: closed - Opened by jakevc over 1 year ago - 2 comments

#527 - [GEN-720] support new SV primary keys

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago

#526 - Do not cross-file validate if ancillary files not present

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago

#525 - Add in support for ancilliary files in cli

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago - 1 comment

#524 - [GEN-706] Cross-validate clinical assay information

Pull Request - State: closed - Opened by rxu17 over 1 year ago - 1 comment

#523 - [GEN-561] Add cross validation to check for seq-assay-id bed file pair

Pull Request - State: closed - Opened by rxu17 over 1 year ago - 1 comment

#522 - [GEN-562] Cross-validate maf with clinical sample files

Pull Request - State: closed - Opened by rxu17 over 1 year ago - 2 comments

#521 - Add mypy pre-commit

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago - 1 comment

#520 - [GEN-560] Add ancillary files for cross-validation

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#519 - [GEN-694] Remove fusions from dashboarding

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago

#517 - Add in pre-commit

Pull Request - State: closed - Opened by thomasyu888 over 1 year ago

#516 - [GEN-636] Allow NAs/blanks for unrequired columns in SV

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#515 - [GEN-564] Add support for more values for site1 site2 col in SV file

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#514 - [GEN-493] Accept Unknown for SV dna and rna support columns

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#512 - MAF file validation

Issue - State: open - Opened by jakevc over 1 year ago - 1 comment

#511 - [GEN-568] Create sv case list

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#510 - [GEN-429] Validate chromosome columns in bed file

Pull Request - State: closed - Opened by rxu17 over 1 year ago - 1 comment

#509 - [GEN-428] Validate chromosome column in SV

Pull Request - State: closed - Opened by rxu17 over 1 year ago

#508 - 15.1.0-rc

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#507 - [GEN-496] remove fusions file support

Pull Request - State: closed - Opened by rxu17 almost 2 years ago

#506 - [GEN-506] Support new synapser client - Update installation

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#505 - [GEN-497] Remove fusion file from consortium release

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#503 - [GEN-445] Allow for NA values SV files

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#502 - [GEN-427] Use validation_chrom function for maf

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago - 1 comment

#501 - [GEN-426] Use new function to validate chromosome for SEG file

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago - 1 comment

#500 - [GEN-290] Write dup variants

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago - 1 comment

#499 - [GEN-424, GEN-423] Allow MT chromosome to be specified

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#498 - [GEN-416] Pin dependency versions

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#497 - [GEN-407] Check GENIE genome nexus instance

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#496 - [GEN-258] Update SV validation

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#495 - [GEN-413] Update GENIE VCF validation

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#494 - [GEN-413] Add more vcf validation rules

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#493 - [GEN-412] Add renv and better installation/testing instructions

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#492 - [GEN-299] add load module

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#491 - [GEN-324] use conftest throughout tests

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago - 1 comment

#490 - [GEN-323] remove unused classes

Pull Request - State: closed - Opened by thomasyu888 almost 2 years ago

#489 - [GEN-295] Add extract.py module

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#488 - [GEN-285] hotfix - make sure release folder fileview is indexed

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#487 - [GEN-258] Update structural variant validation

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#486 - Prepare release 14.3.0

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#485 - v14.3.0 release candidate

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#483 - [GEN-185] Fusions entrez gene must be integers

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#482 - [GEN-177] HOTFIX - Lock down pandas version

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago

#481 - [GEN-174] allow for patch public release versions to be specified

Pull Request - State: closed - Opened by thomasyu888 about 2 years ago