Funcotator datasource configs should not honor spaces (and some other special characters) in the datasource name nor version.
open | Created 2019-05-14 | Last updated 2019-07-01| Posted by LeeTL1220 | See in Github


Funcotator bug


Bug Report

Affected tool(s) or class(es)

Funcotator

Affected version(s)

All

Description

Since we expect users to write config files manually, we need to have some enforcement of naming rules. At the least, to disallow spaces in the name and version fields. There are many places throughout the code where we assume that there will be no spaces. Additionally, I hear from users that they want any Funcotator tsv outputs to never have spaces (or tabs or other special characters -- "_", "-" are obviously okay).

We can solicit users about which special characters are okay, but definitely disallow spaces and tabs.

Steps to reproduce

Add a space to the Gencode datasource config (name or version field) and try to funcotate a segment file.

Expected behavior

No errors and no spaces in the field names.

Actual behavior

Exception in gene list output renderer.


Return to top