improved checking for upstream deletions in GenotypingEngine #6429
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ldgauthier
approved these changes
Feb 25, 2020
| * Add deletions to a list. | ||
| * Record emitted deletion in order to remove downstream spanning deletion alleles that are not covered by any emitted deletion. | ||
| * In addition to recording a new deletion, this method culls previously-recorded deletions that end before the current variant | ||
| * context. This assumes that variants are traversed in order. | ||
| * | ||
| * @param deletionSize size of deletion in bases |
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Can you note that this is the size for the normalized representation? Otherwise it's not obvious why we need this information in addition to the VC.
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We really didn't need it. I rewrote the method to take in the VC and the emitted alleles.
src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
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@ldgauthier Here's a
GenotypeGVCFsbug fix for you.@tfenne Your suspicion was correct.