jamesemery
jamesemery
Currently the GATK4 version of SplitNCigarReads softclips the overlapping segments of the reads across the split segments. This is a departure from the original GAKT3 behavior which hardclipped the edges....
The recent branch #8489 has demonstrated that there are some problematic edge cases in the pileup allele merging code that could cause pathological numbers of haplotypes to be handed to...
In working on #8296 we have discovered that in the `MafOutputRendererConstants.java` there are myriad constants that hard code aliases with the pattern "Gencode_34_hugoSymbol". This can lead to bad behavior if...
I was using some tasks from here: https://github.com/broadinstitute/long-read-pipelines/blob/dc2cd65fe18e9301925f88cc79a3db601cd38029/wdl/tasks/Utility/Finalize.wdl (specifically FinalizeToDir) and I ran into some esoteric cases where call-caching was failing to re-upload results even when the underlying files had...
When I try to connect to a cromshell server with that I could contact with cromshell 1 by I get the following exception: ``` 2023-07-31 17:01:08,951 cromshell.utilities.http_utils ERROR Failed to...
I have noticed some connectivity issues for the python cromshell environment with some cromsehll servers that otherwise work on the older cromshell... however i have noticed that I can no...
When I am working with Cromshell frequently and I have to do a lot of swapping between servers to connect with I very often find myself having to maintain a...
I have noticed an intermittent failure in my experiments using Readfish + Barcode-Dependent target lists that seems to trigger between 0-3 times per 72 hour sequencing experiment. Always Readfish will...