[MISC] Move parse_cigar from format_sam_base into cigar.

[Irallia]

Resolves first part of seqan/iGenVar#85

We decided to move parse_cigar from seqan3::detail::format_sam_base into seqan3/io/sam_file/detail/cigar.hpp.
This is still detail, but now you normaly just need to include one header. Apon this, it is also easier to get everything to do with cigar out of detail later.

[vercel]

This pull request is being automatically deployed with Vercel (learn more).
To see the status of your deployment, click below or on the icon next to each commit.

🔍 Inspect: https://vercel.com/seqan/seqan3/UyjfeBYSUBVkrN1LoQHFHmaoq1H6
✅ Preview: https://seqan3-git-fork-irallia-misc-iomoveparsecigarintocigarhpp-seqan.vercel.app

[codecov]

Codecov Report

Merging #2502 (fe462a6) into master (c40960b) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #2502   +/-   ##
=======================================
  Coverage   98.22%   98.22%           
=======================================
  Files         269      269           
  Lines       10510    10517    +7     
=======================================
+ Hits        10323    10330    +7     
  Misses        187      187           

Impacted Files	Coverage Δ
...lude/seqan3/io/sam_file/detail/format_sam_base.hpp	97.82% <ø> (-0.20%)	⬇️
include/seqan3/io/sam_file/detail/cigar.hpp	97.75% <100.00%> (+0.78%)	⬆️
include/seqan3/io/sam_file/format_bam.hpp	96.21% <100.00%> (ø)
include/seqan3/io/sam_file/format_sam.hpp	97.08% <100.00%> (ø)
include/seqan3/io/record.hpp	100.00% <0.00%> (ø)
include/seqan3/io/sequence_file/input.hpp	100.00% <0.00%> (ø)
include/seqan3/io/sequence_file/output.hpp	100.00% <0.00%> (ø)
include/seqan3/argument_parser/validators.hpp	91.39% <0.00%> (ø)
include/seqan3/io/sequence_file/format_fastq.hpp	100.00% <0.00%> (ø)
include/seqan3/io/sequence_file/input_options.hpp	100.00% <0.00%> (ø)
... and 3 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update c40960b...fe462a6. Read the comment docs.

[simonsasse]

This static void does not appear in the include/seqan3/io/sam_file/detail/cigar.hpp. Is it just unnecessary ? :)

[Irallia]

As the function is not in a class anymore, I think the static is not necessary.

[eseiler]

A static member of a class would mean that the member (in this case a member function) is independent of the actual object. Maybe think of it as "there is one (global) instance of this member" and the member exists without any instance of the class existing.

It also means that you do not need an instance of the format_sam_base (or any derived) class to invoke this function. You can use format_sam_base::update_alignment_lengths instead of some_instance.update_alignment_lengths.

[simonsasse]

Thanks for the explanation. Looks good :)