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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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nogls.t2 test fails #941

Open mmokrejs opened 4 years ago

mmokrejs commented 4 years ago

Hi, I just installed gemini and ran the test suite but it fails with:

 nogls.t2
1,4c1,4
< chrom start   end variant_id  gene    family_id   family_members  family_genotypes    samples family_count    violation   violation_prob
< chr1  10670   10671   1   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) G/G,G/G,G/C NA12877 1   plausible de novo   0.96228
< chr1  28493   28494   2   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) T/C,T/T,C/C NA12877 1   loss of heterozygosity  0.65973
< chr1  28627   28628   3   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) C/C,C/C,C/T NA12877 1   plausible de novo   0.98859
---
> chrom start   end variant_id  gene    family_id   family_members  family_genotypes    samples family_count    violation
> chr1  10670   10671   1   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) G/G,G/G,G/C NA12877 1   plausible de novo
> chr1  28493   28494   2   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) T/C,T/T,C/C NA12877 1   loss of heterozygosity
> chr1  28627   28628   3   None    CEPH1463    NA12889(NA12889;unknown;male),NA12890(NA12890;unknown;female),NA12877(NA12877;unknown;male) C/C,C/C,C/T NA12877 1   plausible de novo
fail

The last commit is bc84fe2