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Put hts_ prefix in front of various klib functions #881

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wants to merge 4 commits into from
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Put hts_ prefix in front of various klib functions #881

wants to merge 4 commits into from

Commits on Jun 10, 2019

  1. Put hts_ prefix in front of kstring funcs and add wrappers for API 

    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)
    @daviesrob
    daviesrob committed Jun 10, 2019
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  2. Upgrade kmemmem to take size_t long strings and add tests 

    Pattern is limited to size INT_MAX.

Fix memory leak found by tests.
    @daviesrob
    daviesrob committed Jun 10, 2019
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  3. Put hts_ prefix in front of kfunc functions and add wrappers 

    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.
    @daviesrob
    daviesrob committed Jun 10, 2019
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  4. Put hts_ prefix in front of knetfile funcs and add wrappers 

    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.
    @daviesrob
    daviesrob committed Jun 10, 2019
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