Updated some of the qmotif documentation, adding the ini section, and adding an explanation of the elements in the summary section.
Fixed a bug where if you run in includes_only: false mode on GRCh38, you get a "Too many open files" error as it creates (and I guess opens) SAMFileReader objects for all the contigs in the genome, of which there are lots for GRCh38.
Some minor mode that my trusty copilot suggested.
Type of change
[X] Bug fix (non-breaking change which fixes an issue)
[X] This change requires a documentation update
How Has This Been Tested?
Unit tests pass.
New code was run against a COLO BAM and compared to the output of the existing code run against the same BAM. They were identical.
Are WDL Updates Required?
No. No new options names etc
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
Updated some of the qmotif documentation, adding the ini section, and adding an explanation of the elements in the summary section.
Fixed a bug where if you run in includes_only: false mode on GRCh38, you get a "Too many open files" error as it creates (and I guess opens) SAMFileReader objects for all the contigs in the genome, of which there are lots for GRCh38.
Some minor mode that my trusty copilot suggested.
Type of change
How Has This Been Tested?
Unit tests pass. New code was run against a COLO BAM and compared to the output of the existing code run against the same BAM. They were identical.
Are WDL Updates Required?
No. No new options names etc
Checklist: