Align assemblies autothreading

[lynnjo]

Description

Provide a summary of your changes including motivation and context.
If these changes fix a bug or resolves a feature request, be sure to link to that issue.

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• CHANGE (fix or feature that would cause existing functionality to not work as expected)
• FEATURE (non-breaking change which adds functionality)
• BUGFIX (non-breaking change which fixes an issue)
• ENHANCEMENT (non-breaking change which improves existing functionality)
• NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have updated relevant documentation

Changelog entry

Please add a one-line changelog entry below. This will be copied to the changelog file during the release process.
made total-threads and in-parallel optional parameters for align-assemblies

made total-threads and in-parallel optional parameters for align-assemblies

[codecov]

Codecov Report

Attention: 23 lines in your changes are missing coverage. Please review.

Comparison is base (4fdf8b1) 87.19% compared to head (8292319) 86.52%.
Report is 2 commits behind head on main.

❗ Current head 8292319 differs from pull request most recent head c4d1e26. Consider uploading reports for the commit c4d1e26 to get more accurate results

Files	Patch %	Lines
...lin/net/maizegenetics/phgv2/cli/AlignAssemblies.kt	71.60%	18 Missing and 5 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #72      +/-   ##
==========================================
- Coverage   87.19%   86.52%   -0.67%     
==========================================
  Files          22       22              
  Lines        2077     2145      +68     
  Branches      285      300      +15     
==========================================
+ Hits         1811     1856      +45     
- Misses        152      170      +18     
- Partials      114      119       +5     

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