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bailey-lab / MIPTools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
https://miptools.readthedocs.io
MIT License
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Sample groups #57

Closed alfredsimkin closed 5 months ago

alfredsimkin commented 5 months ago

Charlie converted the sample_groups variable (in yaml files) to a sample_set variable. This solves the following problems with the sample_groups variable:

  1. sample_groups grabs both the sample_set and the probe_set as a list (instead of as separate variables)
  2. it requires an exact match to the probe_set column, resulting in the potential exclusion of valid samples (e.g. if a user inputs ['JJJ', 'DR1,VAR4'] then any matches to JJJ with 'DR1,VAR5' would be ignored.
  3. it makes the assumption that there might be multiple probe sets to analyze (inherent in being a list) when in reality our variant calling system can only handle one probeset at a time
  4. it's completely redundant with the probe_set variable (which actually specifies the probe set a user wants to analyze), which also confuses new users.
alfredsimkin commented 5 months ago

created this pull request on Charlie's behalf after reviewing changes, which I'm now approving