The primary purpose of this branch—at least at first—was to make off-target analysis, recently added to the end-to-end workflow (#143), optional.
While testing, I started updating the HTML report to handle thresholds more gracefully. I ended up going down a rabbit hole and touching more code than I expected. But I think overall it improved the relevant code throughout the codebase. The CLI is no longer neutral on thresholds by default, and getting rid of None and empty string defaults cleaned up the implementation a bit. And the report now shows a table of thresholds unconditionally, whether a per-marker config file was specified or not.
Still to do:
[x] implement tests for new parsing function
[x] update documentation to indicate that GRCh38 coordinates are optional, but will disable certain features when absent
Closes #141.
[x] Changes are clearly described above
[x] Any relevant issue threads are referenced in the description
[x] Any new features are tested (see the development manual for details)
The primary purpose of this branch—at least at first—was to make off-target analysis, recently added to the end-to-end workflow (#143), optional.
While testing, I started updating the HTML report to handle thresholds more gracefully. I ended up going down a rabbit hole and touching more code than I expected. But I think overall it improved the relevant code throughout the codebase. The CLI is no longer neutral on thresholds by default, and getting rid of
Noneand empty string defaults cleaned up the implementation a bit. And the report now shows a table of thresholds unconditionally, whether a per-marker config file was specified or not.Still to do:
Closes #141.