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Is your feature request related to a problem? Please describe.
Will be nice to convert genotypes in forward coding format. This will be useful to transform data in other format like VCF
Describe the solution you'd like
The ideal solution will be working with datasets separately, by converting genotypes in temporary files (and folders)
Describe alternatives you've considered
An alternative, will be working on the final dataset and doing the conversion using the SNPconvert.py tool. This will be easier since the data are in the same format and less changes are required to maintain this project
Additional context
Ideally, this task should do:
Convert from illumina to forward in src.features.smarterdb.Location
Add a _to_forward function in src.features.plinkio.SmarterMixin
Support src and dst coding in src.features.plinkio.SmarterMixin._process_genotypes , _process_pedline and update_pedfile
Is your feature request related to a problem? Please describe.
Will be nice to convert genotypes in forward coding format. This will be useful to transform data in other format like VCF
Describe the solution you'd like
The ideal solution will be working with datasets separately, by converting genotypes in temporary files (and folders)
Describe alternatives you've considered
An alternative, will be working on the final dataset and doing the conversion using the
SNPconvert.py
tool. This will be easier since the data are in the same format and less changes are required to maintain this projectAdditional context
Ideally, this task should do:
src.features.smarterdb.Location
_to_forward
function insrc.features.plinkio.SmarterMixin
src.features.plinkio.SmarterMixin._process_genotypes
,_process_pedline
andupdate_pedfile
SNPconvert.py
bcftools
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