Put hts_ prefix in front of various klib functions #881
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Prevent clashes with other libraries that use the Attactive Chaos version of kstring.h by putting an hts_ prefix in front of all the external symbols. The API is preserved by adding static inline wrappers around the renamed symbols. Relatively trivial functions ksprintf(), kstrstr() and kstrnstr() are moved into the header file. Fixes samtools#693 (Duplicate symbols with libbwa)
Pattern is limited to size INT_MAX. Fix memory leak found by tests.
Prevent clashes with other libraries that use the Attactive Chaos version of kfunc.h by putting an hts_ prefix in front of all the external symbols. The API is preserved by adding static inline wrappers around the renamed symbols. Changes a few leading underscores to trailing ones.
Also makes all functions in knetfile.c that are not included in the knetfile.h header static as they are not part of the public api.
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IMHO this complexity is a mistake. HTSlib is the 800-pound gorilla here. #693 could be very easily worked around in bwa, as suggested in #693 (comment). People using the Attractive Chaos versions of gamma functions etc who add HTSlib usage to their project can be expected to use the HTSlib-supplied versions of such functions and remove their own copied-in klib headers. And rather than contemplate such changes in knetfile.[ch], perhaps it is time to remove them from HTSlib (as services are said to be moving to HTTPS, which knetfile does not support, and knetfile has long been superseded by hfile_libcurl in HTSlib). |
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Put hts_ prefix in front of various klib functions and add wrappers to preserve the existing API. This is so we don't get clashes with the Attarctive Chaos versions of these functions, in case anyone links against both.
Fixes #693 (Duplicate symbols with libbwa)
N.B. Breaks ABI, so
TWO_TO_THREE_TRANSITION_COUNTneeds to be incremented on merge (which should not be done as a fast-forward).