(SV) Add tests for AssemblyContigWithFineTunedAlignments #4961
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fix a bug in AssemblyContigWithFineTunedAlignments.getReasonForAlignmentClassificationFailure() * also apprently RDD collected list is unmodifiable; forgot to make new before sorting * close a group of sam file writers
Codecov Report
@@ Coverage Diff @@
## master #4961 +/- ##
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+ Coverage 80.76% 80.795% +0.034%
- Complexity 17930 17947 +17
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Files 1094 1094
Lines 64523 64524 +1
Branches 10392 10392
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+ Hits 52109 52132 +23
+ Misses 8386 8370 -16
+ Partials 4028 4022 -6
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Also fixes small bugs.