Comments (1)
Thank you for the suggestions.
-
The tool bgenix supports transformation into the VCF format, so maybe we can use that for creating a test dataset. There already is minimal code for reading
.gen
,.vcf
, and.haplotype
files in the test code at this time, so maybe you can use that if necessary. -
Yes,
probabilities!
andminor_allele_dosge!
are allocating for every variant, and this can be avoided by using internal functions at this time. I may have to restructure/document these functions for the last suggestion.
from bgen.jl.
Related Issues (12)
- Cannot get ref/alt allele label for haplotype data HOT 2
- Read all ALT allele as 1 and REF allele as 0 in `minor_allele_dosage!`? HOT 1
- Always treat REF as `major_allele` and ALT as `minor_allele` HOT 2
- TagBot trigger issue HOT 16
- maf, hwe, info_score, counts! for general cases
- Individual ID extracted from wrong column HOT 2
- convert to called genotypes HOT 7
- minor_allele_dosage!'s outputs oscillates for some variants HOT 3
- Importing haplotypes.bgen throws assertion error HOT 1
- Typo for haplotype documentation HOT 2
- Features to add HOT 20
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from bgen.jl.