Makes IntervalKeepPairFilter filter out single ended reads #1252
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Codecov Report
@@ Coverage Diff @@
## master #1252 +/- ##
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+ Coverage 69.366% 69.384% +0.018%
- Complexity 8155 8158 +3
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Files 548 548
Lines 32702 32702
Branches 5522 5522
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+ Hits 22684 22690 +6
+ Misses 7798 7794 -4
+ Partials 2220 2218 -2
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@lbergelson could you please take a look at this? |
lbergelson
requested changes
Jan 7, 2019
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@meganshand One comment about the test. Looks good otherwise. If you can address that then 👍
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| final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList); | ||
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| boolean singleEnded = StreamSupport.stream(builder.spliterator(), false) |
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It looks like this might be cleaner if you use builder.getRecords().stream() instead of this spliterator path.
Also, instead of assertingFalse it might be cleaner to use noneMatch and have one less inversion.
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On further inspection you're just copying the pattern around it... maybe we can fix them all in a separate PR. |
lbergelson
approved these changes
Jan 7, 2019
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@meganshand Thank you for this! |
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Description
When a BAM contains both single ended and paired ended reads this filter throws an exception (
java.lang.IllegalStateException: Inappropriate call if not paired read). Since the filter is only meant to keep paired reads it now also filters out single ended reads and doesn't throw an exception.Checklist