Option for vg call to select reference paths by sample name #4031
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Outdated suggestions cannot be applied.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.
Changelog Entry
To be copied to the draft changelog by merger:
-S
option added tovg call
to select reference paths by sample name. This is more convenient as it allows, ex-S GRCh38
to be used in place of-p GRCh38#0#chr1 -p GRCh38#0#chr2 ..
. Such selection is necessary when the graph has more than one reference sample andvg call
will now refuse to handle graphs with multiple reference samples unless paths are selected with-S
or-p
.Description
This is critical for calling on the v1.1 HPRC graphs, which contain both GRCh38 and CHM13 as reference samples. Whereas running
call
without any path selection worked fine on the v1.0 graphs (which had a single reference sample), it makes a big mess on the newer graphs as it calls on both references at once...