Local_to_global: local alleles not strictly increasing: [0,2,1]

Hail Query & hailctl
1

Hello,

I’m using the function hl.vds.local_to_global() to convert LAD to AD, and got this error “Error summary: HailException: local_to_global: local alleles not strictly increasing: [0,2,1]”. Do you know what would be the cause? Thanks!

Here is my command in case helpful.

mt = vds.variant_data.annotate_entries(
    AD = hl.vds.local_to_global(vds.variant_data.LAD, 
                                vds.variant_data.LA, 
                                n_alleles=hl.len(vds.variant_data.alleles), 
                                fill_value=0, 
                                number='R')
)
2

Hmm. I’m not sure what the issue is. Let me tag in our VDS expert, @tpoterba .

3

is this an AoU VDS? Can you share the script so we know any transormatinos that occurred between the read and error?

4

Yes, this is an AoU VDS. The script is simple. Just read vds and then transform. Thanks for checking!
vds = hl.vds.read_vds(vds_path)
mt = vds.variant_data.annotate_entries(
AD = hl.vds.local_to_global(vds.variant_data.LAD,
vds.variant_data.LA,
n_alleles=hl.len(vds.variant_data.alleles),
fill_value=0,
number=‘R’)
)

5

In case it is helpful, I can successfully convert LGT to GT in the same vds using hl.experimental.lgt_to_gt().

6

I think this is a bug in hl.vds.local_to_global – I was too strict making this check in order to generate slightly faster code.

Here’s a tracking issue:

I hope to have some time to make a patch this afternoon

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