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Funcotator - Need to have a funcotation output list #4359

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jonn-smith opened this issue Feb 6, 2018 · 3 comments
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Funcotator - Need to have a funcotation output list #4359

jonn-smith opened this issue Feb 6, 2018 · 3 comments
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@LeeTL1220
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Funcotator
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Engine-2Q2018

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@jonn-smith
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Must allow support for an output funcotation list that, if specified, will cause Funcotator only output funcotations from the given list and suppress all other funcotations.
@jonn-smith jonn-smith added this to the Engine-4.1 milestone Feb 6, 2018
@jonn-smith jonn-smith self-assigned this Feb 6, 2018
@jonn-smith jonn-smith modified the milestones: Engine-4.1, Engine-1Q2018 Feb 6, 2018
@droazen droazen modified the milestones: Engine-1Q2018, Engine-2Q2018 Apr 6, 2018
@jonn-smith jonn-smith assigned LeeTL1220 and unassigned jonn-smith May 15, 2018
@jonn-smith
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This is related to #4583 - that issue must be done before this one is worked on.

@LeeTL1220
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LeeTL1220 commented Jun 26, 2018 •
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  • Add a CLI flag --exclude-field-name which can be specified multiple times.
    For example ... --exclude-field-name Clinvar_bar --exclude-field-name Clinvar_foo ...

We will specify the column names with the full field name: <datasourcename>_<fieldname>

For now, we specify via an exclude. If nothing is specified, then show everything.

@jonn-smith
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Put exclusion list into OutputRenderer at construction time, then check on write.

LeeTL1220 added a commit that referenced this issue Sep 26, 2018
@LeeTL1220
Adding exclusion lists (#4359) and sanitizing MAF field values (#4693)…
6e59fca 
…. Added some developer utilities for ease of testing and creating new Funcotations.
@LeeTL1220 LeeTL1220 mentioned this issue Sep 26, 2018
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LeeTL1220 added a commit that referenced this issue Sep 29, 2018
@LeeTL1220
Adding command line exclusion lists, so that users can prune fields f…
dc59aab 
…rom output. (#5226)

- Added support for `--exclusion-list` parameter, which can be specified multiple times.  This will remove some rendered fields from the output.  The field should appear exactly as written in the output MAF or VCF (e.g. ClinVar_ALLELEID). Closes #4359. 
- Does basic cleaning of field values for MAF.  I.e. cleaning tabs and \n.  Fixes #4693
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