[feat] Add an option to sort by sequence role in CollectAlternateContigNames

[nh13]

This is so that I can have assembled molecules first, whereas in some assembly reports chrM (an assembled molecule) is listed at the end of the report.

[codecov-commenter]

Codecov Report

Merging #868 (bbacea4) into main (da9ecbc) will decrease coverage by 0.09%.
The diff coverage is 22.22%.

@@            Coverage Diff             @@
##             main     #868      +/-   ##
==========================================
- Coverage   95.66%   95.56%   -0.10%     
==========================================
  Files         125      125              
  Lines        7239     7246       +7     
  Branches      507      514       +7     
==========================================
  Hits         6925     6925              
- Misses        314      321       +7     

Flag	Coverage Δ
unittests	95.56% <22.22%> (-0.10%)	⬇️

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Impacted Files	Coverage Δ
...umgenomics/fasta/CollectAlternateContigNames.scala	85.54% <22.22%> (-7.88%)	⬇️

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