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poseidon-framework / poseidon-analysis-hs

A tool to analyse genotype data (optionally in the poseidon data format)
MIT License
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Header/content inconsistency in `xerxes fstats` tableOutFile #3

Closed TCLamnidis closed 2 years ago

TCLamnidis commented 2 years ago

The header for the tableOutFile contains column names formatted for F4 stats. But F3 statistics are printed without an extra empty column d, shifting the values of the table by one field.

Example f4 output:

Statistic   a   b   c   d   Estimate    StdErr  Z score
F4(<ind0>,Pop0,Pop1,Ref)    <ind0>  Pop0    Pop1    Ref -3.917282594233266e-4   2.824200272990533e-4    -1.3870413623624762

Example f3 output:

Statistic   a   b   c   d   Estimate    StdErr  Z score
F3vanilla(<ind0>,<ind1>,Ref)    <ind0>  <ind1>  Ref 0.12017712575708295 1.281349541666742e-3    93.78949447374059

Reading the output of F3 into a table will result in the Estimate field ending up under the d header, StdErr in the Estimate field and so on.

xerxes v0.1.2.2 for poseidon v2.5.0

TCLamnidis commented 2 years ago

Same goes when running F2 (essentially):

Statistic       a       b       c       d       Estimate        StdErr  Z score
F3vanilla(<ind0>,<ind0>,Ref)    <ind0>  Ref     0.30095376926280704     1.481348932258261e-3    203.16197130139642
stschiff commented 2 years ago

Ah I know, but I think I fixed that in the latest version. Are you using the conga-version? I should update that then. Will happen when I declare the next version update.