Support external tabixpp #375
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
This fixes a canonicalization check that was looking at span instead of SVLEN. It also checks against canonicalizing variants whose end positions would fall outside the contig. Those are incorrect in the VCF and can't safely be canonicalized.
|
Thanks! |
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Outdated suggestions cannot be applied.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.
On top of #374, this fixes the CMake configuration so that an external tabixpp library can actually be used if found. It makes sure to use the associated CFLAGS from pkg-config for tabixpp and htslib.
It also makes sure that
CMAKE_C_FLAGSandCMAKE_CXX_FLAGSdon't get completely replaced for release builds, in case they are set on the CMake command line.