Optimize intervals fails to merge abutting intervals #979
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| @@ -42,10 +42,10 @@ public int compareTo(final QueryInterval other) { | |||
| } | |||
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| /** | |||
| * @return true if both are on same reference, and other starts exactly where this ends. | |||
| * @return true if both are on same reference, and other starts exactly before this ends. | |||
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I don't think we should be changing the definition of "abuts". since we use closed intervals the implementation was correct before the change.
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@yfarjoun If QueryInterval really uses closed intervals, then I think @Kirvolque is right and the existing implementation was wrong. E.g. two closed intervals 1-9 and 10-20 abut one another, but the coordinates are indeed off by one.
That said, I think this method should be private since it doesn't test bi-directionally. That's fine given how it's used in optimizeOverlaps, but it would be confusing if called by other code.
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Ahh, I see. Sorry to judge so quick. The method is called from BAMFileReader, so it can't be changed to private. perhaps we just change it's name to something like endAtStartOf so that the code would read prev.endsAtStartOf(nextInterval).
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@yfarjoun, thank you. The method has been renamed.
Kirvolque
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@yfarjoun, thank you for quick response. If offered changes are unnecessary, may we close this pull request? |
| @@ -94,4 +94,24 @@ public String toString() { | |||
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| return unique.toArray(EMPTY_QUERY_INTERVAL_ARRAY); | |||
| } | |||
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| @Override | |||
| public boolean equals(Object o) { | |||
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In classes that implement Comparable it's preferable to implement equals() as this.compareTo(that) == 0 after the initial type checks.
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@tfenne, done. Thank you for your note.
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Please note that there are a few failures in the tests...testQueryOverlappingMultipleIntervals fails in 3 cases (probably because they were written using the wrong definition of "abutting" :-) |
fix: Fix tests for previous behaviour of abuts method refactor: Change abuts method name to endsAtStartOf
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This looks better to me. @tfenne ? |
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LGTM. I think the failed check is due to a random error contacting ENA in one of the tests. I've restarted it. Once it passes I'll merge. |
Codecov Report
@@ Coverage Diff @@
## master #979 +/- ##
==============================================
- Coverage 65.938% 65.927% -0.01%
Complexity 7459 7459
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Files 529 529
Lines 31956 31964 +8
Branches 5460 5462 +2
==============================================
+ Hits 21071 21073 +2
- Misses 8743 8749 +6
Partials 2142 2142
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Kirvolque
changed the title
Description
Optimizing intervals in
QueryIntervalclass works incorrectly: intervals are considered abutting only if they overlap each other by a single base.Prerequisites
Need bug fix for current implementation of abuts():
QueryInterval[]array still contains two initial intervals after invokingoptimizeIntervals()method, even though they touch. Github issue.Solution
abuts()method has been fixed. It used to returntrueonly in case if one of them starts exactly where other ends. Now it returnstrueif one of the given intervals ends just before another one starts;equals()andhashcode()methods were overridden inQueryIntervalclass for usingassertin TestNg;testOptimizeIntervals()was added to theCRAMFileBAIIndexTestclass to test 3 options: abutting, overlapping and non-overlapping intervals.Checklist