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Strand bias doesn't get exported #1226

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fnothaft opened this issue Oct 25, 2016 · 3 comments
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Strand bias doesn't get exported #1226

fnothaft opened this issue Oct 25, 2016 · 3 comments
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@fnothaft
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Similar to #1203, Strand bias does not get properly exported on conversion back to VCF.
@fnothaft fnothaft added the bug label Oct 25, 2016
@heuermh
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heuermh commented Oct 27, 2016

Are you referring to VCF INFO reserved key SB?
The corresponding field was intentionally removed from Variant in recent changes.

@fnothaft
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Format key, not info.

@heuermh
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heuermh commented Oct 27, 2016

I see, so you're saying the fix in #1203 was only on the read side, not the write side.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 7, 2016
@fnothaft
[ADAM-1226] Properly export strand bias components.
74046d6 
Resolves bigdatagenomics#1226. Adds logic to
`org.bdgenomics.adam.converters.VariantContextConverter` that checks for a
4 element array in the `strandBiasComponents` field. If this is present, this
is exported as the "SB" VCF field.
@fnothaft fnothaft mentioned this issue Nov 7, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Nov 8, 2016
@fnothaft
[ADAM-1226] Properly export strand bias components.
33a601a 
Resolves bigdatagenomics#1226. Adds logic to
`org.bdgenomics.adam.converters.VariantContextConverter` that checks for a
4 element array in the `strandBiasComponents` field. If this is present, this
is exported as the "SB" VCF field.
@heuermh heuermh closed this as completed in 93585e5 Nov 8, 2016
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@heuermh @fnothaft