Commits on Jun 27, 2024

1. Speed up faidx. …

   - bgzf_getc is slow as it's a heavy function and not inlined.  Most of
     the time though it's just an array fetch, so inline the basic form and
     revert to the function call for the complex form.
   
   - isgraph and all other ctype functions are slow.  We assume ASCII and
     just do a naive implementation.
   
   The speed benefits are (seconds):
   
                         Old     New
       Index GRCh38      13.4    8.4
       Query chr1	       1.7    0.9
   
   Given a significant speed change for a small localised modification it
   seems worth while having.

   

   jkbonfield committed Jun 27, 2024
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