Fix an instance of non-determinism in HaplotypeCaller #6104
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lbergelson
commented
Aug 20, 2019
lbergelson
commented
- Fixing a non-deterministic point in HaplotypeCaller's KBestHaplotypeFinder
- It uses a priority queue to compare scores, if there are ties the tie breaking is arbitrary and seems to be different depending on circumstances of the run.
- For some as of yet unknown reason reading from a gs path vs a local path can cause this to be triggered.
- Adding a tie breaker which uses the entirety of the bases in the Path in cases where the score is tied, this is unique per path.
* Fixing a non-deterministic point in HaplotypeCaller's KBestHaplotypeFinder * It uses a priority queue to compare scores, if there are ties the tie breaking is arbitrary and seems to be different depending on circumstances of the run. * For some as of yet unknown reason reading from a gs path vs a local path can cause this to be triggered. * Adding a tie breaker which uses the entirety of the bases in the Path in cases where the score is tied, this is unique per path. Co-authored-by: jamesemery <[email protected]> Co-authored-by: Louis Bergelson <[email protected]>
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Hopefully a fix for #6105 |
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Uhhh... I'm not really sure how to write a test for non-deterministic behavior... especially that behavior that we don't fully understand. We certainly need to see if this actually fixes some of the larger scale jitter we have witnessed. |
…rator creation out as a static object
lbergelson
commented
Aug 21, 2019
...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
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…otypecaller/graphs/KBestHaplotypeFinder.java
lbergelson
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jamesemery
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Aug 23, 2019
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I honestly don't think its very easy or really possible to test this branch properly. @droazen
This was referenced Oct 15, 2020
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