Migrate from tbb to onetbb

[lkeegan]

• add FlexbarAtomic
  • a simple wrapper around std::atomic which adds a copy constructor
  • to replace tbb::atomic member variables in classes with default copy constructors
• replace removed tbb::atomic
  • with FlexbarAtomic if copy constructor was assumed
  • with std::atomic otherwise
• filters (PairedAlign, PairedInput, PairedOutput)
  • no longer inherit from tbb::filter
  • take and return pointers to actual type instead of void*
  • operator() is now const
• pipeline
  • use parallel_pipeline and make_filter
• use global_control to set max threads
• use oneapi::tbb namespace
• add find_package for TBB to CMakeLists.txt

[tillea]

I've tested this patch with the Debian package and confirm flexbar builds that way. Unfortunately the test seems to end in some endless loop:

 cd test ; \
 export PATH="/build/flexbar-3.5.0/obj-x86_64-linux-gnu:$PATH" ; \
 echo $PATH ; \
 export HOME=/tmp ; \
 which flexbar ; \
 ./flexbar_test.sh
 /build/flexbar-3.5.0/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin
 /build/flexbar-3.5.0/obj-x86_64-linux-gnu/flexbar

 Testing fasta:

Hopefully someone will be able to fire up gdb and find a fix. Kind regards, Andreas.

[lkeegan]

@tillea thanks for testing - I didn't notice the tests folder! 1c872fa10 should fix the endless loop and another issue that came up with the pipeline changes, and now the tests pass for me

[tillea]

This works for me now and I'll upload the Debian package with these patches. Thanks a lot, Andreas.