[MISC] Remove field::alignment from sam_file_[in/out]out.

[smehringer]

Also Fixes #2907

Deprecation warning:

The most readable solution is to add a static assert. Otherwise I would have to deprecate the field::alignment. But then we couldn't use it once we implement e.g. Blast or MSA IO.
So I just wanted to deprecate using it with the SAM file.

In file included from /home/svenja/AGABI/seqan3/test/snippet/io/sam_file/sam_file_input_reading_structured_bindings.cpp:4:
/home/svenja/AGABI/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input<seqan3::sam_file_input_default_traits<>, seqan3::fields<seqan3::field::alignment, seqan3::field::mapq>, seqan3::type_list<seqan3::format_sam> >’:
/home/svenja/AGABI/seqan3/test/snippet/io/sam_file/sam_file_input_reading_structured_bindings.cpp:19:95:   required from here
/home/svenja/AGABI/seqan3/include/seqan3/io/sam_file/input.hpp:260:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information.
  260 |     static_assert(!selected_field_ids::contains(field::alignment),

Todo:

• Check documentation

Follow Up:

• Do we need to pass the reference sequences now that the field::alignment is gone
• Remove field::offset

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Name	Status	Preview	Updated
seqan3	✅ Ready (Inspect)	Visit Preview	Nov 1, 2022 at 11:09AM (UTC)

[codecov]

Codecov Report

Base: 98.24% // Head: 98.22% // Decreases project coverage by -0.01% ⚠️

Coverage data is based on head (049eb2f) compared to base (334b790).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3058      +/-   ##
==========================================
- Coverage   98.24%   98.22%   -0.02%     
==========================================
  Files         275      275              
  Lines       12346    12197     -149     
==========================================
- Hits        12129    11981     -148     
+ Misses        217      216       -1     

Impacted Files	Coverage Δ
include/seqan3/alphabet/cigar/cigar.hpp	90.90% <ø> (ø)
include/seqan3/io/sam_file/detail/cigar.hpp	100.00% <ø> (+1.96%)	⬆️
...lude/seqan3/io/sam_file/detail/format_sam_base.hpp	97.85% <ø> (-0.12%)	⬇️
include/seqan3/io/sam_file/header.hpp	100.00% <ø> (ø)
include/seqan3/io/sam_file/input.hpp	100.00% <ø> (ø)
...nclude/seqan3/io/sam_file/input_format_concept.hpp	100.00% <ø> (ø)
include/seqan3/io/sam_file/output.hpp	100.00% <ø> (ø)
...clude/seqan3/io/sam_file/output_format_concept.hpp	100.00% <ø> (ø)
include/seqan3/io/sam_file/record.hpp	100.00% <ø> (ø)
include/seqan3/io/sam_file/sam_flag.hpp	100.00% <ø> (ø)
... and 7 more

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[eseiler]

If you feel like it, you can replace all occurrences of counter++;

LGTM, rebase + auto-merge :)

[smehringer]

please do not merge yet. I think a better deprecation warning for the record is needed.

[smehringer]

@eseiler Can you please have a look at sam_file/record.hpp again

[eseiler]

Is there a way to dispatch to alignment_from_cigar, i.e. do we get access to the reference sequence from here somehow?

[smehringer]

no, since

1. It would require some dirty hacking to give extra data to the tuple (record)
2. there is no guarantee that a reference sequence is provided.