[tree] allow VCF input without exclude-sites arg #565
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
Previous behavior expected that any VCF input would have a (bed-like) exclude-sites file, however this is should not be necessary. This commit allows such functionality, resulting in a FASTA for tree-building with no positions removed.
Codecov Report
@@ Coverage Diff @@
## master #565 +/- ##
=======================================
Coverage 20.92% 20.92%
=======================================
Files 31 31
Lines 5133 5133
Branches 1300 1300
=======================================
Hits 1074 1074
Misses 4007 4007
Partials 52 52
Continue to review full report at Codecov.
|
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Outdated suggestions cannot be applied.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.
Previous behavior expected that any VCF input to
augur treewould have a (bed-like) exclude-sites file, however this is should not be necessary. This commit allows such functionality, resultingin a FASTA for tree-building with no positions removed.
P.S. If you wish to achieve this behavior before this PR is merged you can do so by creating an empty file without a
.bedextension and passing that to--exclude-sitesTesting
No testing implemented.
Tested locally by removing the
--exclude-sites {input.sites}argument from this test.