Closed michaelgatzen closed 1 year ago
Merging #1616 (d564490) into master (489c419) will increase coverage by
0.022%
. The diff coverage is81.633%
.
@@ Coverage Diff @@
## master #1616 +/- ##
===============================================
+ Coverage 69.840% 69.862% +0.022%
- Complexity 9684 9696 +12
===============================================
Files 703 703
Lines 37752 37770 +18
Branches 6131 6139 +8
===============================================
+ Hits 26366 26387 +21
+ Misses 8932 8928 -4
- Partials 2454 2455 +1
Impacted Files | Coverage Δ | |
---|---|---|
...mtools/util/IntervalListReferenceSequenceMask.java | 72.973% <33.333%> (+2.703%) |
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...va/htsjdk/samtools/util/AbstractLocusIterator.java | 69.945% <50.000%> (-1.004%) |
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...in/java/htsjdk/samtools/util/EdgeReadIterator.java | 82.090% <92.105%> (+4.731%) |
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src/main/java/htsjdk/samtools/util/Interval.java | 70.000% <0.000%> (+3.333%) |
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.../htsjdk/samtools/util/AbstractRecordAndOffset.java | 84.615% <0.000%> (+3.846%) |
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...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java | 90.476% <0.000%> (+9.524%) |
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@lbergelson Thanks for the review, and all the deep digging you did for that! I addressed most of the comments, feel free to comment or resolve the threads!
getCurrentInterval()
to determine the read overlaps. However, thelastInterval
that it uses internally was never updated. This PR removes the methodgetCurrentInterval()
and instead implements this functionality inEdgeReadIterator
, which is the only place this has ever been called from (at least in Picard and GATK). This is arguably a breaking API change, although I would argue that this method has never worked and should not be placed in AbstractLocusIterator, but instead in an iterator implementation that actually does keep track of the intervals.