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updating to newer htsjdk snapshot #3588
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👍 looks good to me
@jean-philippe-martin We're seeing the same errors here as in yours pr. So it's something in the htsjdk update... |
@lbergelson @jean-philippe-martin I looked into this it a bit - it can be readily reproduced if the failing test is run through gradle, but not from IntelliJ, which is because when it runs through gradle, its using asyncIO for BAM writing, but when run from IntelliJ its using sync io. I'm not sure why this issue is showing up now, but in the cases that fail, the async writer thread is being interrupted by this code which is called from the main thread when the PrintReads closeTool method closes the writer (I added a trace statement to verify this). When I run in IntelliJ and force async io to be used, the interrupt call still happens, but there is no test failure. |
One short term option would be to turn off async writing until we figure out the right fix. |
The regression was introduced in samtools/htsjdk@1ade6c9 |
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Codecov Report
@@ Coverage Diff @@
## master #3588 +/- ##
==============================================
+ Coverage 79.738% 79.98% +0.242%
- Complexity 18153 18896 +743
==============================================
Files 1221 1222 +1
Lines 66623 68248 +1625
Branches 10411 10916 +505
==============================================
+ Hits 53124 54585 +1461
- Misses 9290 9367 +77
- Partials 4209 4296 +87
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the htsjdk regression was fixed in samtools/htsjdk#992 |
@jean-philippe-martin I've updated the htsjdk snapshot, you should be unblocked after a rebase. |
Thank you very much @lbergelson ! |
updating to a new htsjdk snapshot and updating our VariantContextWriters to compile
test may fail on this....