bbimber

exactly. i also didnt know this was possible, but bcftools apparently can do it. it would be very useful to be able to get variant count like this for big...

all of our indexes are made by tabix and have this info, which makes sense if bcftools/tabix share the same code

Hello - sorry to bug but is there a chance someone would be willing to look at this PR? It's a bugfix designed to make seurat-disk compatible with the latest...

Our workflow just started to intermittently hit this as well. Our workflow in question uploads two artifacts, one ~250mb and one under 100. Some of the time they both work,...

@ivirshup I'm happy to try to share just the h5ad file (which isnt huge); however, here is some R code using public data that should do it. Again, at least...

I am guessing lines like this break it: ``` MT RefSeq exon 536 607 . + . gene_id ""; transcript_id "unknown_transcript_1"; gbkey "tRNA"; product "tRNA-Phe"; exon_number "1"; ``` note the...

@hextraza Let's discuss this script. Thinking aloud: if the primary scenario we want to support is headless CI, or perhaps the scenario where we want to build our local LK...

Thanks, we were actually just talking about this option. It does seem like maybe that would be the easiest.

@mlathara see below. after running this, I realized there is now a separate --genomicsdb-max-alternates argument, which i've added on subsequent runs. How does --max-genotype-count related to --genomicsdb-max-alternates? ``` /home/exacloud/gscratch/prime-seq/java/java8/bin/java \...

@mlathara thanks for the detailed reply. I will start adding "--genomicsdb-max-alternates-alleles" as three greater than --max-alternates, as recommended. It seems like it would be useful is GenotypeGVCFs defaulted to this...