hail
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import_plink cannot read files with out-of-order variants
to replicate:
mt = hl.balding_nichols_model(10, 10, 10)
hl.export_plink(mt.key_cols_by(s=hl.str(mt.sample_idx)), '/tmp/foo')
then manually edit bim file to look like:
1 1:1:A:C 0.0 1 C A
1 1:2:A:C 0.0 2 C A
1 1:3:A:C 0.0 3 C A
1 1:4:A:C 0.0 4 C A
1 1:5:A:C 0.0 5 C AA
1 1:6:A:C 0.0 5 C AAAAA
1 1:7:A:C 0.0 5 C T
1 1:8:A:C 0.0 5 C GGGG
1 1:9:A:C 0.0 5 C G
1 1:10:A:C 0.0 5 C A
then
hl.import_plink(bed='/tmp/foo.bed', bim='/tmp/foo.bim', fam='/tmp/foo.fam', min_partitions=10)