ZipperBams to produce mate score ("ms") for samtools markdup

[nh13]

Fixes: #951

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (9c475fd) 95.62% compared to head (87e8288) 95.62%.
Report is 8 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff            @@
##             main     #952    +/-   ##
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  Coverage   95.62%   95.62%            
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  Files         126      126            
  Lines        7354     7454   +100     
  Branches      502      491    -11     
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+ Hits         7032     7128    +96     
- Misses        322      326     +4     

Flag	Coverage Δ
unittests	95.62% <100.00%> (+<0.01%)	⬆️

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[tfenne]

I don't object in principal, but these should all probably be of the form:

primary.get[Int]("AS").foreach(supp("ms") = _)

so that it will work for aligners that don't produce an AS tag and on pairs where only one read is aligned.

[tfenne]

LGTM but could you add/amend a couple of tests to make sure it works on both reads that have and don't have AS set?

[TedBrookings]

Sorry for the delay. Looks good to me