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Funcotator: deal with delimiters in data for output formats #4693

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droazen opened this issue Apr 23, 2018 · 3 comments
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Funcotator: deal with delimiters in data for output formats #4693

droazen opened this issue Apr 23, 2018 · 3 comments
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@LeeTL1220
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Funcotator
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Engine-2Q2018

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@droazen
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droazen commented Apr 23, 2018 •
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Eg., need to escape or otherwise deal with ;, ,, |, etc. characters in datasource values when writing to VCF.
@droazen droazen added this to the Engine-2Q2018 milestone Apr 23, 2018
@jonn-smith
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This needs to happen for MAF too.

We should add a method OutputRenderer::sanitizeField that we can plug into the annotation process that will automatically sanitize each field for illegal characters as they are added to the output. This will require refactoring the OutputRenderer::write method to be concrete with a call to another write method and this sanitizeField method to get the benefits automatically for all OutputRenderers.

@LeeTL1220
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This is done for VCF only when #4838 is merged.

@jonn-smith
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Need to add for MAF in the \t case.

@jonn-smith jonn-smith changed the title Funcotator: deal with special characters in output formats Funcotator: deal with delimiters in data for output formats Sep 25, 2018
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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@droazen @LeeTL1220 @jonn-smith