feature/cached-aligner bugfix

[TimD1]

This fixes most off-by-one errors, but there are still ArrayIndexOutOfBounds errors thrown every few hundred thousand alignments.

[codecov]

Codecov Report

Attention: Patch coverage is 66.66667% with 4 lines in your changes missing coverage. Please review.

Project coverage is 95.51%. Comparing base (a44f400) to head (02ccad2).

Files with missing lines	Patch %	Lines
.../scala/com/fulcrumgenomics/alignment/Aligner.scala	66.66%	4 Missing ⚠️

Additional details and impacted files

@@                    Coverage Diff                     @@
##           feature/cached-aligner    #1024      +/-   ##
==========================================================
- Coverage                   95.59%   95.51%   -0.08%     
==========================================================
  Files                         126      126              
  Lines                        7722     7406     -316     
  Branches                      501      507       +6     
==========================================================
- Hits                         7382     7074     -308     
+ Misses                        340      332       -8     

Flag	Coverage Δ
unittests	95.51% <66.66%> (-0.08%)	⬇️

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