Ian Fiddes
Ian Fiddes
Is there a reason for that line to be there? What would be the implications of just removing it?
I have never seen this error. If it happening with the SS file too, I would suggest asking the phast people for help and showing them a minimal SS file...
What does the output of `halStats $hal` say?
That looks normal to me. Does this happen with all MAFs extracted from this HAL? I assume you are extracting a whole-genome MAF. What happens if you slice it up?
Any update on this?
To add detail to my use case: I am using gipc to create a split-run-join paradigm. Within a gevent WSGI environment, I need to spawn some number of jobs that...
That makes sense, but pileup.c still writes this out with fileformat=VCF4.1 https://github.com/ifiddes/htsbox/blob/lite/pileup.c#L337 And yes, the concern is backwards compatibility. I can replace the `R` with `.` by hand in my...
The offending alignment is this: ```113676 45 0.829 6.410E-05 39 0 40 527 566 585 39 0 0 584 27M1I12M1D``` Which does appear to be walking off the end to...
I am having a hard time creating a minimal reference sequence to reproduce the crash. If I reduce the target database down to only the aligned sequence, it doesn't happen....
I was unable to make a minimal ref, so I uploaded the ref to Box. It is a human and mouse transcriptome. I had to break it into three parts,...