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Attribute getters should be migrated from GATKProtectedVariantContextUtils to VariantContext (HTSJDK) #5454

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TedBrookings opened this issue Nov 28, 2018 · 0 comments
Open

Attribute getters should be migrated from GATKProtectedVariantContextUtils to VariantContext (HTSJDK) #5454

TedBrookings opened this issue Nov 28, 2018 · 0 comments
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@lbergelson
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Feature request

Tool(s) or class(es) involved

GATKProtectedVariantContextUtils
VariantContext (HTSJDK)

Description

There are currently multiple attribute getters in GATKProtectedVariantContextUtils that properly belong in VariantContext and should be migrated. Some are nearly duplicates (with subtly different default/missing value handling) and some have no counterpart (getAttributeAsLong and getAttributeAsLongArray). Due to the potential for conflict, this issue should likely not be finished until the getters in HTSJDK are fixed (samtools/htsjdk#1228).
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@lbergelson @TedBrookings