count-sv groups BED queries by chr and not chr_start_end #7
Description
When I call count-sv with a 3-column BED file like this:
athena count-sv --query-format bed -o DEL.counts.tsv gnomad_v3.sv.filtered.DEL.sites.vcf.gz gene_desert_coords_chr22.bed
Where gene_desert_coords_chr22.bed looks like this:
#chr start end
chr22 1 100001
chr22 100001 200001
chr22 200001 300001
chr22 300001 400001
chr22 400001 500001
...
I get this output grouped by chr:
#query n_svs
. 0
chr22 1689
When I'm expecting it to be grouped by row or chr_start_end. Possibly something to do with the last commit which is named Extend count-sv to work for gtf and generic BED?
The workaround is to just add a fourth column name in the format chr_start_end to make those groupings manually, which works fine.