merge: Support sequences without cross-checking #1631
Draft
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
victorlin
changed the title
--sequences + --output-sequences
|
Closing – the latest plan is to support at least some form of optional cross-checking. |
|
Re-opening per #1579 (comment). I'll incorporate some newer developments from #1601 before opening for review. |
victorlin
force-pushed
the
victorlin/merge-sequences-separately
branch
3 times, most recently
from
83c70cf to
a367d19
Compare
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1631 +/- ##
==========================================
+ Coverage 73.06% 73.11% +0.04%
==========================================
Files 79 79
Lines 8335 8398 +63
Branches 1700 1721 +21
==========================================
+ Hits 6090 6140 +50
- Misses 1958 1965 +7
- Partials 287 293 +6 ☔ View full report in Codecov by Sentry. |
From preview review: <#1601 (comment)> Co-authored-by: John SJ Anderson <[email protected]>
Preparing for use across functions. It can still be conditionally set as the first thing in run() because that is the entrypoint.
Preparing for use across functions.
Preparing for sequence support.
This will be used for sequence merge.
In addition to the existing metadata support. SeqKit is used to deduplicate across sequence files and check for duplicates within an individual sequence file. Co-authored-by: Thomas Sibley <[email protected]>
victorlin
force-pushed
the
victorlin/merge-sequences-separately
branch
from
44218f9 to
fe72fac
Compare
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Outdated suggestions cannot be applied.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.
Description of proposed changes
Add sequence support in
augur merge.Related issue(s)
Closes #1579
Checklist