Avoid conflicting with HTSlib's kstring.c functions #346
Conversation
This file contains hidden or 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
Make ksprintf() static inline in kstring.h, so that it (like the other bwa/kstring.h functions) won't conflict with similar HTSlib functions. Instead implement it and kvsprintf() in terms of a new bwa_kvsprintf() function. Fixes samtools/htslib#693.
e69bf8c to
b52164f
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.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.
Some people's programs use both HTSlib and libbwa.a — see e.g. samtools/htslib#693. Unfortunately one function —
ksprintf— is defined in both libraries, leading to linker errors.This happens for
ksprintfonly, because all the other functions in bwa's kstring.h are declared asstatic inline.This PR makes
ksprintf()static inline in kstring.h, so that it (like the other bwa/kstring.h functions) won't conflict with similar HTSlib functions. Instead implement it and a newkvsprintf()in terms of a newbwa_kvsprintf()function. Fixes samtools/htslib#693.