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Rename n_bins to probes in genemetrics output #586

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merged 1 commit into from
Mar 25, 2021

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tskir
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@tskir tskir commented Mar 24, 2021

Closes #585. Thank you @eriktoo for reporting and investigating this.

The column n_bins in the genemetrics output means exactly the same thing as probes in regular CNS files. For compatibility, it is better if they are named the same. This would also allow feeding genemetrics CNS files to the call and export commands.

The column `n_bins` in the genemetrics output means exactly the same
thing as `probes` in regular CNS files. For compatibility, it is better
if they are named the same. This would also allow feeding genemetrics
CNS files to the call and export commands (see etal#585).
@tskir
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tskir commented Mar 24, 2021

Note: in theory, n_bins is a name which better reflects reality than probes. However, it's much easier to change it in this direction, since renaming probes to n_bins would involve quite a lot of changes throughout the pipeline which I'd rather not do at this stage.

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etal commented Mar 25, 2021

This looks like a good solution, thanks!

@etal etal merged commit b55ef86 into etal:master Mar 25, 2021
@tskir tskir deleted the fix-genemetrics-column-name branch May 9, 2021 21:44
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cnvkit export vcf does not work when nbins is used instead of probes in cns header
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