Fix for donor assignment negative infinity likelihoods.

[jamesnemesh]

Fix for edge case bug where multiple reads are summarized as a single UMI with a single phred score. Due to the underlying error rating being quantized by the pred score, a very high error rate of 0.9 or higher is quantized to a phred score of 0. This is equivalent to an error rate of 1 when the phred score is unpacked to a probability, which causes errors with the downstream likelihoods.

To fix this, during summarization, if the phred score is less than 1 it is set to 1. This avoids issues in the likelihood calculations where having probabilities of 0 causes issues when logged (plus probabilities should always include some uncertainty, which is lost if a phred score is 0.)

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 80.65%. Comparing base (825b982) to head (655fa4c).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
...digitalallelecounts/SummarizeUMIBaseQualities.java	50.00%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##             master     #477      +/-   ##
============================================
- Coverage     80.65%   80.65%   -0.01%     
  Complexity     4690     4690              
============================================
  Files           358      358              
  Lines         20030    20032       +2     
  Branches       3118     3119       +1     
============================================
  Hits          16156    16156              
- Misses         2608     2609       +1     
- Partials       1266     1267       +1     

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