samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Fixing zero-length interval bug in IntervalList.merge #1318

Closed lbergelson closed 5 years ago

lbergelson commented 5 years ago

Fixing a bug in IntervalList.merge() that caused it to break when merging 0 length intervals
Improving tests for merge
The bug was introduced in #1265 and hasn't been in any release

Checklist

[ ] Code compiles correctly
[ ] New tests covering changes and new functionality
[ ] All tests passing
[ ] Extended the README / documentation, if necessary
[ ] Is not backward compatible (breaks binary or source compatibility)

codecov-io commented 5 years ago

Codecov Report

Merging #1318 into master will not change coverage. The diff coverage is 100%.

@@             Coverage Diff             @@
##              master     #1318   +/-   ##
===========================================
  Coverage     67.635%   67.635%           
  Complexity      8230      8230           
===========================================
  Files            562       562           
  Lines          33617     33617           
  Branches        5642      5642           
===========================================
  Hits           22737     22737           
  Misses          8706      8706           
  Partials        2174      2174

Impacted Files	Coverage Δ	Complexity Δ
...c/main/java/htsjdk/samtools/util/IntervalList.java	`74.754% <100%> (ø)`	`75 <0> (ø)`	:arrow_down:

lbergelson commented 5 years ago

I added some more test cases to cover the cases you mentioned

lbergelson commented 5 years ago

@yfarjoun I added the tests I think you wanted. Is there anything else?

lbergelson commented 5 years ago

@yfarjoun There exists problems with 0-length intervals... Unsurprisingly... I've opened a pr draft #1320 that shows some of them. I'm not going to resolve them in this PR.

yfarjoun commented 5 years ago

👍