-flip-to-match-cohort1 / -match-alleles-to-cohort1 issues

Issue #64 new
Gavin Band
repo owner created an issue

1: The docs currently call this option -match-alleles-to-cohort1, but actually it's called -flip-to-match-cohort1. (The latter is more similar to -flip-to-match-allele that is used with a strand file to reorient data, so maybe that's a better name.)

2: Currently (v2.0.1) -flip-to-match-cohort1 won't work unless you also don't match variants by alleles. E.g. this will work:

qctool_v2.0.1 -g test1.gen -g test2.gen -flip-to-match-cohort1 -og - -compare-variants-by position,rsid

but this won't:

qctool_v2.0.1 -g test1.gen -g test2.gen -flip-to-match-cohort1 -og -

Comments (2)

  1. Gavin Band reporter

    NB. the source of the 2nd issue is in the implementation of VariantIdentifyingData::CompareFields, in particular operator() and is_equal() which do not handle the flipping correctly.

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