Fix/update seqan3

[SGSSGene]

• Updates submodule seqan3 to newest master.
• Adds sharg as a submodule
• replaces all seqan3 argument parsing functionality with sharg

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +1.05 🎉

Comparison is base (8787850) 85.51% compared to head (743f0c2) 86.57%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #134      +/-   ##
==========================================
+ Coverage   85.51%   86.57%   +1.05%     
==========================================
  Files           4        4              
  Lines         863      931      +68     
==========================================
+ Hits          738      806      +68     
  Misses        125      125              

Impacted Files	Coverage Δ
include/shared.h	100.00% <100.00%> (ø)
src/main.cpp	93.92% <100.00%> (+1.94%)	⬆️

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[mr-c]

What's the plan on merging this?

When I build needle 1.0.1 with Seqan3 3.3.0 RC1, I get the following test errors:

	  2 - test/api/estimate_test (NUMERICAL)
	  3 - test/api/ibf_test (NUMERICAL)
	  4 - test/api/ibfmin_test (NUMERICAL)
	  5 - test/api/minimiser_test (NUMERICAL)

Starting program: /build/seqan-needle-1.0.1.0.1.git.439eeab+ds/obj-x86_64-linux-gnu/test/api/estimate_test 
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Running main() from ./googletest/src/gtest_main.cc
[==========] Running 10 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 10 tests from estimate
[ RUN      ] estimate.small_example

Program received signal SIGFPE, Arithmetic exception.

0x00005555555d262e in sdsl::int_vector<(unsigned char)0>::resize (value=0, size=<error reading variable: Division by zero>, this=0x7fffffffd210)
    at /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp:527
527	    void resize(const size_type size, const value_type value) { bit_resize(size * m_width, value);

Starting program: /build/seqan-needle-1.0.1.0.1.git.439eeab+ds/obj-x86_64-linux-gnu/test/api/ibf_test 
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Running main() from ./googletest/src/gtest_main.cc
[==========] Running 8 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 8 tests from ibf
[ RUN      ] ibf.given_expression_thresholds

Program received signal SIGFPE, Arithmetic exception.
0x000055555557303e in sdsl::int_vector<(unsigned char)0>::resize (value=0, size=<error reading variable: Division by zero>, this=0x7fffffffd810)
    at /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp:527
527	    void resize(const size_type size, const value_type value) { bit_resize(size * m_width, value); }

[mr-c]

Okay, 743f0c2 fixed building needle w/ Seqan3 3.3.0

[mr-c]

Ping :-)

[eseiler]

Partially resolved by #144
We still need to replace the seqan3 argument parser with sharg.
Packaging also needs some care, because we are using CPM.