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Fix import_plink contig_recoding defaults #4926

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merged 3 commits into from Dec 7, 2018

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@jigold
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@jigold jigold commented Dec 7, 2018

Fixes #4925.

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@tpoterba tpoterba left a comment

looks great, but one possible orthogonal enhancement

@@ -1631,7 +1628,10 @@ def import_plink(bed, bim, fam,
contig_recoding : :obj:`dict` of :obj:`str` to :obj:`str`, optional
Dict of old contig name to new contig name. The new contig name must be
in the reference genome given by ``reference_genome``.
in the reference genome given by ``reference_genome``. If ``None``, the
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@tpoterba tpoterba Dec 7, 2018

not totally in-scope, but can we add a warning above that if you have GRCh38, PLINK probably encodes your data as 1, 2, 3 and needs a recoding?

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@tpoterba tpoterba Dec 7, 2018

actually, should we just use this as the default recoding?

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@jigold jigold Dec 7, 2018

That seems fine to me.

@danking danking merged commit b9537d1 into hail-is:master Dec 7, 2018
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4 participants