Update htscodecs for new SIMD code + gcc-12 fixes #1438
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gcc-12.1 produced a warning that NULL could be passed to strcmp() via str_class. I'm not sure if that can actually happen, but just in case add a check.
Update htscodecs to bring in the rANS 32x16 codecs Add new htscodecs source files and dependencies into htslib makefiles. Some htscodecs functions have changed name slightly so a couple of cram source files are updated to reflect that. These changes are enough to build the non-SIMD versions of the new codecs, but don't enable the accelerated versions yet.
Adds the checks necessary to detect x86_64 SIMD support and turn it on the htscodecs if it's available. As ssse3, popcnt and sse4.1 are used together, they're tested for as a group.
For the benefit of htslib embeds that don't want to create and run a configure script. Adds a small script that does a similar job by probing a few compiler options and then outputs makefile lines to set variables if they succeed. These lines are added to the default 'htscodecs.mk' file that gets built if configure hasn't already made one. Adding them here means the probing will be remembered until the next "make distclean". The script fragment that builds the default 'config.h' checks to see if the variables have been set, and if so adds the appropriate 'HAVE_' lines for the feature.
Mainly to ensure that the fuzzer build doesn't start complaining about unaligned access.
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Updates the htscodecs submodule and adds changes necessary to make HTSlib build the new SIMD codec implementations. Also includes a somewhat unrelated gcc-12 fix in
vcf.cneeded to make the tests work.configure.acgets new checks for the various options needed to generate SIMD code.Makefilerules are updated to make the new object files, and add SIMD options to only the ones that need them. The rules that run the compiler get an extraTARGET_FLAGSvariable so flags can be adjusted on a per-target basis even if the user setsCFLAGSon the command line (which stops the Makefile from overriding it).A small script is added to probe compiler options on non-configure builds, allowing them to enable the SIMD code. The compiler tests are the same as for
configureand have been written so that they don't generate warnings and work even if the user sets-WerrorinCFLAGS.