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AlphaGenes / AlphaPeel

AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
MIT License
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Ensure map file input is handled properly when not sorted in ascending order #155

Open XingerTang opened 5 months ago

XingerTang commented 5 months ago

see discussion in #154

gregorgorjanc commented 5 months ago

What happens when map file positions (rows) and corresponding genotype file (columns) are not given in ascending order?

Do our calculations handle this out of the box? Do we need to do anything (say, reorder inputs?, change calcs?, ...).

Also, what should we do with the output? Should the output be returned sorted or with the original order?