Fix metabolism coverage bug #1800
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
we kept getting key errors because the gene caller id was a string (for nice printing purposes) rather than an int. nice going, iva [insert sarcastic look here].
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Outdated suggestions cannot be applied.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.
This PR addresses the bugs described in #1798 and #1799.
It really was a very stupid bug. The gene caller id variable which was being used to access the gene coverage information was of type string, when it needed to be an integer, and that was causing KeyErrors. But now it is fixed, and I have tested that all modes are working with the
--add-coverageflag (this includes multi-mode as well!).Additionally, while I was at it, I added the
--add-coveragefunctionality to thekofam_hitsoutput mode (it strangely was not available before; I suppose I forgot it when I was initially coding this). This mode now gets the same coverage and detection columns added as inkofam_hits_in_modulesmode. I have updated the relevant documentation pages to reflect this.Sorry for the inconvenience this bug has caused :)