Fixed MarkDuplicatesSpark so it handles supplementaryReadsWithUnmappedMates properly #4785
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lbergelson
approved these changes
May 18, 2018
| out.add(new Tuple2<>(pass.key(), pass)); | ||
| return out.iterator(); | ||
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| // Mark duplicates cant properly handle templates with more than two reads in a pair |
| File output = createTempFile("supplementaryReadUnmappedMate", "bam"); | ||
| final ArgumentsBuilder args = new ArgumentsBuilder(); | ||
| args.addOutput(output); | ||
| args.addInput(getTestFile("supplementaryReadUnmappedmate.bam")); |
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weird case in the file name, but \shrug
Codecov Report
@@ Coverage Diff @@
## master #4785 +/- ##
==============================================
+ Coverage 80.113% 80.19% +0.078%
- Complexity 17426 17564 +138
==============================================
Files 1082 1082
Lines 63131 63525 +394
Branches 10178 10272 +94
==============================================
+ Hits 50576 50941 +365
- Misses 8567 8582 +15
- Partials 3988 4002 +14
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Before it was resulting in a key collision.