Thomas Yu issues

Results 18 issues of


                                            Thomas Yu

Incorrect Entrez-Hugo Symbol mapping of chr1, 13365776

`vcf2maf.pl` annotates this as ``` Hugo_Symbol Entrez_Gene_Id PRAMEF5 645359 ``` But PRAMEF5 has entrez gene id: 343068, and 645359 is actually PRAMEF26. What is happening here?

Improve contributing guide

[SYNPY-1145] update manifest cli docs

Document Deprecating support for passwords to push towards PAT

Adding support for Link entities in Dataset feature

[SYNPY-620] allow list of user/team ids to be specified in setPermission

There needs to be more thought into how the code is configured here. The nested for loops are not ideal. Release 2.8

[SYNPY-560] set path if file downloaded

This probably requires some more thought. For instance, there could probably be some minor refactor of the `_download_file_entity` to better support all of this. Release 2.8

Deprecate support for passwords, session tokens, and potentially API keys

3.0 release

[SYNPY-925] Remove deprecated property keys

3.0 release

[SYNPY-737] Remove non-standard single dash long cli parameters

This is for a major release 3.0