Fix race condition in SamRecordDuplicateComparator

[fleharty]

Description

The getLibraryId function of SAMRecordDuplicateComparator.java can create race conditions when run multithreaded.

Things to think about before submitting:

• [x] Make sure your changes compile and new tests pass locally.
• [x] Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• [x] Extended the README / documentation, if necessary
• [x] Check your code style.
• [x] Write a clear commit title and message
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  • Breaking changes should be mentioned in the commit message.

[fleharty]

@lbergelson This resolves the race condition thing we discussed the other day. Would you be able to review this?

[codecov-io]

Codecov Report

Merging #1517 into master will increase coverage by 0.038%. The diff coverage is 78.947%.

@@               Coverage Diff               @@
##              master     #1517       +/-   ##
===============================================
+ Coverage     69.343%   69.381%   +0.038%     
- Complexity      8900      8911       +11     
===============================================
  Files            601       601               
  Lines          35503     35511        +8     
  Branches        5901      5901               
===============================================
+ Hits           24619     24638       +19     
+ Misses          8548      8536       -12     
- Partials        2336      2337        +1     

Impacted Files	Coverage Δ	Complexity Δ
...ain/java/htsjdk/samtools/DuplicateSetIterator.java	69.492% <0.000%> (ø)	13.000 <0.000> (ø)
.../htsjdk/samtools/SAMRecordDuplicateComparator.java	68.939% <83.333%> (+10.068%)	54.000 <8.000> (+10.000)
...java/htsjdk/samtools/DuplicateScoringStrategy.java	57.576% <0.000%> (+3.030%)	9.000% <0.000%> (+1.000%)

[fleharty]

@lbergelson I'm unsure about populateTransientAttributes. I can't get it to fail, so as far as I know it is okay. Horror of horrors would be that we do have a sneaky race condition that occurs with very low probability. I'm more than willing to synchronize this method if you think it is necessary, but I have no way of testing that change helps anything.

We depricated SAMRecordDuplicateComparator(final List headers) because it isn't used anywhere internally to HTSJDK, and I'm unaware of any external tools using this constructor.

I don't have permissions to merge this PR. Could you do that for me?

[fleharty]

@lbergelson Back to you.