fix bigwig_outlier_bed handling of qlo #6164
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…w 1MB maximum for linter.
Single select to configure 3 possible outputs. Upper quantile now required. Chide if no low quantile and no output because low not in the choice. Help vastly expanded.
…o need for the user to supply one.
…n since they may not be needed.
makeTableRow renamed
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
|
Can you please bump the version number? |
test outputs are different :(
Yes! Thanks @bgruening - turns out there's a new release and it looks like all the test outputs are a little different. |
|
Scary those changes ... |
nilchia
pushed a commit
to pavanvidem/tools-iuc
that referenced
this pull request
Aug 24, 2024
* adding new tool bigwig_outlier_bed * remove redundant script * replace test.bw with test-data/1.bigwig to decrease test outputs below 1MB maximum for linter. * added bigtools to bio.tools for this new entry added edam * Add a proper version command by importing pybedtools * fix doi for pybigtools * Incorporate Bjoern's ideas. Single select to configure 3 possible outputs. Upper quantile now required. Chide if no low quantile and no output because low not in the choice. Help vastly expanded. * Added the bigwig metadata name as the label for bed feature name so no need for the user to supply one. * Clearing out old test data. Passes tests here but diffs in CI. Something odd. * readding fixed test outputs again again. * Ah. was overwriting a bed with the two bigwig test. * remove print leftovers * Separated python script to enable access for linting in CI * fix flake8 complaints with black on the new separate python script * fix imports * Do not make the output contig statistics table if there's no table output needed. * make the table calculations optional and mostly as a separate function since they may not be needed. * Clean up some comments. makeTableRow renamed * Update tools/bigwig_outlier_bed/.shed.yml Co-authored-by: Björn Grüning <[email protected]> * Update tools/bigwig_outlier_bed/.shed.yml Co-authored-by: Björn Grüning <[email protected]> * Clean up all field prompt text and consolidate the help text into chunks. * remove test for both qhi/qlo because qhi is not optional * fix broken qlo parameter passing and tests - add test for no qlo. * Flake fix * update to 0.2.0 pybigtools test outputs are different :( --------- Co-authored-by: Björn Grüning <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
FOR CONTRIBUTOR:
Tests were producing some empty files because the handling of allowed missing qlo was broken.
This fixes qlo handling; ensures all test diffs are against non-empty samples; and adds a new test for missing qlo.
Update: also bumps to pybigtools 0.2.0 - many test coordinates have changed so need to take a closer look at what it's finding - had assumed it was correct