GroupReadsByUmi only sort input if it is not TemplateCoordinate sorted

[nh13]

This extracts some functionality from #791, where we skip sorting the input if the input is already TemplateCoordinate sorted. This allows other tools to perform the sort.

[codecov-commenter]

Codecov Report

Merging #794 (86e8980) into main (6e0a53d) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #794      +/-   ##
==========================================
+ Coverage   95.51%   95.53%   +0.01%     
==========================================
  Files         122      122              
  Lines        7063     7071       +8     
  Branches      500      505       +5     
==========================================
+ Hits         6746     6755       +9     
+ Misses        317      316       -1     

Flag	Coverage Δ
unittests	95.53% <100.00%> (+0.01%)	⬆️

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Impacted Files	Coverage Δ
...cala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala	95.35% <100.00%> (+0.16%)	⬆️
src/main/scala/com/fulcrumgenomics/bam/Bams.scala	95.72% <0.00%> (+0.85%)	⬆️

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[tfenne]

canTakeNextGroupByUmi on line 480 will, I think, need updating. If the sort was done externally then I don't think we can rely on the fact that they records are also sorted by the same UMI sequence we're going to look at, and so it's not safe to take the next group by UMI.

Usage needs updating to clearly explain when sorting will and won't happen.

[tfenne]

Looks good except for updating usage and fixing up the canTakeNextGroupByUmi.

[nh13]

Done.