Update CI and clang-tidy for BAM support

[AdityaPandeyCN]

• Add libhts-dev across CI jobs
• Move ROOT install into clang-tidy container via install_commands
• Disable false-positive checks for C interop (casting-through-void, reinterpret-cast, branch-clone, header-guard)
• Fix coverage excludes

[AdityaPandeyCN]

The reason to move the ROOT install into the clang-tidy container was because I suspect the old way installed ROOT on the host at /opt/root/, but the container can't see /opt/root/ as only the workspace directory is volume-mounted. So cmake failed silently, compile_commands.json was never generated, causing the headers not identified warnings.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 57.03%. Comparing base (3a3873a) to head (e10090c).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #35      +/-   ##
===========================================
+ Coverage    55.85%   57.03%   +1.17%     
===========================================
  Files           16       16              
  Lines         1425     1394      -31     
  Branches       752      625     -127     
===========================================
- Hits           796      795       -1     
  Misses         521      521              
+ Partials       108       78      -30     

Flag	Coverage Δ
unittests	57.03% <ø> (+1.17%)	⬆️

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see 3 files with indirect coverage changes
see 3 files with indirect coverage changes

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[vgvassilev]

Can you undo all whitespace changes ?

[AdityaPandeyCN]

Done

[vgvassilev]

The commit message does not explain why we suppress these checks.

[AdityaPandeyCN]

added more detail.

[AdityaPandeyCN]

@vgvassilev Please have a look.

[vgvassilev]

How casting-through-void, reinterpret-cast, branch-clone are false positives?

[AdityaPandeyCN]

For casting-through-void , see this (#20 (comment)) was the warning but the bam_aux_append function expects const uint8_t * (https://github.com/samtools/htslib/blob/develop/htslib/sam.h#L1784) and I did static_cast through void* which caused this warning. I cannot think of any other way without this.

[vgvassilev]

For casting-through-void , see this (#20 (comment)) was the warning but the bam_aux_append function expects const uint8_t * (https://github.com/samtools/htslib/blob/develop/htslib/sam.h#L1784) and I did static_cast through void* which caused this warning. I cannot think of any other way without this.

That was a valid issue in the code. You should have fixed your code. In case of bugs we do not suppress the checks but can add a NOLINT comment for the relevant occurrence.

[AdityaPandeyCN]

Apologies for this, have reverted back the suppression