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pheweb parse should automatically sort variants if they aren't sorted. #71

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pjvandehaar opened this issue Apr 11, 2017 · 0 comments
Open

pheweb parse should automatically sort variants if they aren't sorted. #71

pjvandehaar opened this issue Apr 11, 2017 · 0 comments

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@pjvandehaar
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pjvandehaar commented Apr 11, 2017 •
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(We already sort all variants (by MAF) in the QQ plot, so sorting is not too expensive.)

We should sort, but only if we have to. Otherwise, stream. So, PhenoReader.get_variants() asserts sort order. If it fails, it raises NotSorted. The caller catches that and starts over with .get_variants(sort=True) or sort_variants(.get_variants()).
@pjvandehaar pjvandehaar changed the title input_file_parser should automatically sort variants if they aren't sorted. pheweb parse should automatically sort variants if they aren't sorted. May 27, 2017
@pjvandehaar pjvandehaar mentioned this issue Jun 17, 2017
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