Expand post blast recovery #21
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
The first release with this must be a new MAJOR release, as it changes the API for recovery scripts.
1. Create new test data set that can better deomonstrate the BLAST filter 2. Create new test reference / blastDB to match new test dataset 3. Add gitignore rule to ignore user-generated recovery scripts 4. Fix recovery scripts for recoverAll, recoverAmbig, and recoverWrongSpecies 5. Remove chrM_recovery, which is a custom recovery script from our lab 6. Add extra tests to the test config file Next commit will be a substantial restructuring of the retrieveSummary script to make it compatible with runing multiple parameters for the same sample.
And do code cleanup.
NOTE: New Bug: There seems to be a plotting issue in the Depth per Target plot where zero-depth positions are not represented as being zero depth.
Take 1
Take 2
Hotfix for expand_post_blast_recover
scottrk
reviewed
Apr 29, 2020
scottrk
reviewed
Apr 29, 2020
|
I'm trying to be better about only making one set of changes in each branch, but we could do that. |
|
My main concern is: that change is unrelated to the primary purpose of this branch. |
|
That's a good point. It doesn't change functionality, just the complexity of the code, so lower priority. Let's get this out and merge in a fix later. |
|
I have one more branch I want to finish before we go to v2.0.0. Actually, if we're going to do a v1.1.0 release, we should do that before we finish merging this branch. |
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Outdated suggestions cannot be applied.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 will expand options for post-blast recovery, and will clarify some related outputs.